WASHINGTON — President Trump has said he learned lessons from President Richard M. Nixon’s fall from grace, but in using the power of his office to keep his friend and adviser Roger J. Stone Jr. out of prison he has now crossed a line that even Mr. Nixon in the depths of Watergate dared not cross.

For months, senior advisers warned Mr. Trump that it would be politically self-destructive if not ethically inappropriate to grant clemency to Mr. Stone, who was convicted of lying to protect the president. Even Attorney General William P. Barr, who had already overruled career prosecutors to reduce Mr. Stone’s sentence, argued against commutation in recent weeks, officials said.

But in casting aside their counsel on Friday, Mr. Trump indulged his own sense of grievance over precedent to reward an ally who kept silent. Once again, he challenged convention by intervening in the justice system undermining investigators looking into him and his associates, just days after the Supreme Court ruled that he went too far in claiming “absolute immunity” in two other inquiries.

Democrats condemned the commutation of Mr. Stone’s 40-month prison term and vowed to investigate. Speaker Nancy Pelosi, calling the move an act of “staggering corruption,” said she would pursue legislation to prevent the president from using his power to protect those convicted of a cover-up on his own behalf, although that would face serious constitutional hurdles and never be signed into law by Mr. Trump.

Still, Mr. Trump’s action was too much even for some Republican critics of the president, who called it an abuse of power intended to subvert justice. “Unprecedented, historic corruption: an American president commutes the sentence of a person convicted by a jury of lying to shield that very president,” Senator Mitt Romney of Utah wrote on Twitter.

Senator Patrick J. Toomey of Pennsylvania objected too, noting that Mr. Stone was “duly convicted” of obstructing a Republican-led congressional inquiry. “While I understand the frustration with the badly flawed Russia-collusion investigation, in my view, commuting Roger Stone’s sentence is a mistake,” he said. Any objections to his prosecution, he added, “should be resolved through the appeals process.”

Mr. Trump defended his decision after a day at his golf club on Saturday. “Roger Stone was treated horribly,” he told reporters. “Roger Stone was treated very unfairly.” He would not say if he would pardon other campaign advisers, but said the investigators should be prosecuted. “Those are the people that should be in trouble.”

Mr. Trump had long publicly floated the possibility of clemency for allies targeted by prosecutors, including Mr. Stone, his former national security adviser Michael T. Flynn and former campaign chairman Paul Manafort. That by itself was interpreted by critics as witness tampering, in effect promising intervention to allies if they refused to cooperate with investigators against him.

By contrast, one associate who did cooperate, Michael D. Cohen, his former lawyer who arranged hush money for women claiming extramarital affairs with Mr. Trump, was locked up again on Thursday after federal authorities demanded that he agree not to publish a tell-all book in September, deeming it a violation of the terms of his early release.

While Mr. Trump has granted clemency to political allies and others with ties to his White House, he had until now deferred to advisers urging him not to use it for Mr. Stone or others caught up in investigations of the president’s campaign ties to Russia.

Mr. Barr, who has assailed the Russia investigation and moved to drop the case against Mr. Flynn even though he pleaded guilty to lying to the F.B.I., nonetheless objected privately to a commutation for Mr. Stone, officials said. In an interview with ABC News this past week, Mr. Barr said clemency was “the president’s prerogative” but called Mr. Stone’s prosecution “righteous” and the final sentence “fair.” Mr. Trump, who lately has styled himself as a “law and order” president, cut the Justice Department out of his decision, officials said.

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Credit…Samuel Corum for The New York Times

While Republican leaders kept quiet, some of the president’s staunch supporters cheered him on, saying Mr. Trump was properly countering the excesses of overzealous prosecutors.

“In my view it would be justified if President @realDonaldTrump decided to commute Roger Stone’s prison sentence,” Senator Lindsey Graham of South Carolina, chairman of the Senate Judiciary Committee, wrote on Twitter. “Mr. Stone is in his 70s and this was a nonviolent, first-time offense.” (Mr. Stone is actually 67.)

Under the Constitution, the president’s pardon power is expansive, explicitly limited only in that it applies to federal crimes, not to state prosecutions or impeachments. As far back as the 19th century, the Supreme Court ruled that “Congress can neither limit the effect of his pardon nor exclude from its exercise any class of offenders” and as recently as 1974 said the president had “unfettered executive discretion” in granting clemency.

While House Democrats vowed to investigate Mr. Trump’s decision, some lawyers said Congress had no authority to. “I understand the implications for the justice system, but just as a matter of constitutional law, I don’t see how they get into this,” said Stanley M. Brand, a former House counsel under a Democratic speaker.

Still, Mr. Brand and other lawyers said Mr. Stone’s commutation could theoretically be interpreted as an impeachable offense if granted out of corrupt self-interest, although it seemed unlikely that the House would impeach Mr. Trump a second time.

“The president’s pardon power does not extend to nullifying the rule of law for his own cronies to shield from public scrutiny his own obstruction of justice,” said Harold Hongju Koh, a Yale Law School professor and lawyer in President Barack Obama’s administration.

The history of presidential clemency is replete with disputes over the propriety of relief from the nation’s highest office.

Just days before the 1992 election, Lawrence E. Walsh, the independent counsel investigating the Iran-contra affair, filed a new indictment against former Defense Secretary Caspar W. Weinberger revealing notes contradicting President George Bush’s account of his involvement. Mr. Bush considered that a dirty trick by Mr. Walsh to influence the election and indeed he was defeated days later.

Mr. Bush responded the next month to what he considered an illegitimate prosecution by pardoning Mr. Weinberger and five others, prompting Mr. Walsh to complain that “the Iran-contra cover-up, which has continued for more than six years, has now been completed.”

President Bill Clinton issued a raft of more than 175 pardons or commutations on his last day in office in 2001, including for his own half brother Roger Clinton and several former administration officials. Also pardoned was Susan H. McDougal, a former business partner from Arkansas who spent 21 months behind bars for refusing to cooperate with the independent counsel Ken Starr’s investigation of the Whitewater land venture.

Unlike the case with Mr. Stone, Mr. Clinton acted only after Ms. McDougal had already served her sentence and been released. With the Whitewater investigation wrapped up, Mr. Clinton faced no legal risk at that point.

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Credit…Kamenko Pajic/Associated Press

The bigger furor arose over his pardon of the financier Marc Rich, who had fled the country to avoid charges of evading $48 million in taxes and obtained clemency after his ex-wife, Denise Rich, a Democratic donor, contributed money to Mr. Clinton’s presidential library. Democrats joined Republicans in condemning the pardon and Mr. Clinton later expressed regret because of “the terrible politics.”

Jack L. Goldsmith, a Harvard Law School professor and Justice Department official under President George W. Bush, said those cases could be seen as parallels to Mr. Stone’s commutation but pointed to the larger pattern under Mr. Trump. In 31 of his 36 pardons or commutations, he noted, Mr. Trump advanced his political goals or benefited someone with a personal connection, whose case had been brought to his attention by television or was someone he admired for their celebrity.

“This has happened before in a way,” Mr. Goldsmith said. “But there has been nothing like Trump from a systematic perspective.”

John Q. Barrett, a former Iran-contra prosecutor, said Mr. Trump’s action was more objectionable than Mr. Bush’s. “This is much, much more brazen and almost transactionally criminal,” he said in an email. “Deferred payment for toughing it out/silence.”

One president who dared not use his pardon power in such a way was Mr. Nixon, although he considered it. Mr. Nixon’s associates paid hush money and dangled the prospect of clemency to the Watergate burglars to buy their silence but that was off the table once the Watergate story broke open.

Likewise, Mr. Nixon secretly promised to pardon three lieutenants, H.R. Haldeman, John D. Ehrlichman and John N. Mitchell, the day after Senate hearings opened in 1973. “I don’t give a shit what comes out on you or John, even that poor, damn, dumb John Mitchell,” he told Mr. Haldeman in a conversation captured on his taping system. “There is going to be a total pardon.”

Mr. Haldeman sensed danger. “Don’t even say that,” he warned.

“Forget you ever heard it,” Mr. Nixon replied.

He never followed through. Mr. Haldeman, Mr. Ehrlichman and Mr. Mitchell were indicted in 1974 and accused of making “offers of leniency, executive clemency, and other benefits” to obstruct justice. All three went to prison.

Mr. Nixon resigned that August without using his pardon pen. But he received one himself a month later from President Gerald R. Ford, who wanted to spare the country the spectacle of a former president on trial, only to trigger a backlash that helped cost him the 1976 election.

“I think Nixon understood the power of the public and did his crimes in private, not in public, to avoid political consequences,” said Jill Wine-Banks, a Watergate prosecutor. “He was right then. Look what happened to Ford. But Trump sees no consequences.”

Maggie Haberman and Sharon LaFraniere contributed reporting.