The decision will disappoint the human rights community and members of his own party who complained during the Trump administration that the U.S. was failing to hold Mohammed bin Salman accountable, but as the double standards in Biden administration is the new-norm, what was wrong when Trump did it, became right when Biden is doing it.

President Biden has decided that the diplomatic cost of directly penalizing Saudi Arabia’s crown prince, Mohammed bin Salman, is too high, according to senior administration officials, despite a detailed American intelligence finding that he directly approved the killing of Jamal Khashoggi, the dissident and Washington Post columnist who was drugged and dismembered in October 2018.

The decision by Mr. Biden, who during the 2020 campaign called Saudi Arabia a “pariah” state with “no redeeming social value,” came after weeks of debate in which his newly formed national security team advised him that there was no way to formally bar the heir to the Saudi crown from entering the United States, or to weigh criminal charges against him, without breaching the relationship with one of America’s key Arab allies.

Officials said a consensus developed inside the White House that the cost of that breach, in Saudi cooperation on counterterrorism and in confronting Iran, was simply too high.

For Mr. Biden, the decision was a telling indication of how his more cautious instincts kicked in, as the responsibilities of managing a difficult ally led him to find ways other than going directly after Prince Mohammed to make Saudi Arabia pay a price.

While human rights groups and members of his own party applauded the president for making public the official intelligence finding, whose contents leaked more than two years ago, many said that it was just a first step — and that more had to be done to hold the crown prince, known by his initials M.B.S., accountable for his role.

Many organizations were pressing Mr. Biden to, at a minimum, impose the same travel sanctions against the crown prince as the Trump administration imposed on others involved in the plot.

Mr. Biden’s aides said that as a practical matter, Prince Mohammed would not be invited to the United States anytime soon, and they denied that they were giving Saudi Arabia a pass, describing series of new actions on lower-level officials intended to penalize elite elements of the Saudi military and impose new deterrents to human rights abuses.

Those actions, approved by Secretary of State Antony J. Blinken, include a travel ban on Saudi Arabia’s former intelligence chief, who was deeply involved in the Khashoggi operation, and on the Rapid Intervention Force, a unit of the Saudi Royal Guard that protects Prince Mohammed — and is under his direct control.

The declassified intelligence report concluded that the intervention force directed the operation against Mr. Khashoggi at the Saudi Consulate in Istanbul. Mr. Khashoggi entered the consulate on Oct. 2, 2018, to get papers he needed for his forthcoming marriage, and, with his fiancée waiting outside the gates, was instead met by an assassination team.

An effort by the Saudi government to issue a cover story, contending that Mr. Khashoggi had left the consulate unharmed, collapsed in days.

The Trump administration acted against 17 members of that team, imposing travel bans and other penalties. Mr. Biden, one official said, described the new sanctions the United States is imposing to King Salman, the crown prince’s father, in a phone call on Thursday that was only vaguely described in a White House account of the call.

But the king is 85 and in poor health, and it was unclear to administration officials how much he absorbed as Mr. Biden talked about a “recalibration” of the relationship with the United States.

In an effort to signal wider action against countries and officials who reach beyond their borders to repress dissent, Mr. Blinken is also adding a category of sanctions, a newly named “Khashoggi ban,” to restrict visas to anyone determined to be participating in state-sponsored efforts to harass, detain or harm dissidents and journalists around the world. In a statement, Mr. Blinken said 76 Saudis would be designated in the first tranche.

That review, officials said, would be part of the annual State Department human rights report. It is part of an effort, officials said, to create a new category of human rights abuses — one called “extraterritorial repression,” a growing issue as Russia, China and even allies like Turkey try to silence critics who are living in Europe, the United States or other free societies.

While the initial bans will apply to Saudis, officials said they would quickly be used around the world.

A few hours after the release of the report and the new sanctions, the Saudi government issued a blistering response. “The kingdom of Saudi Arabia completely rejects the negative, false and unacceptable assessment in the report pertaining to the kingdom’s leadership, and notes that the report contained inaccurate information and conclusions,” it wrote.

“It is truly unfortunate that this report, with its unjustified and inaccurate conclusions, is issued while the kingdom had clearly denounced this heinous crime, and the kingdom’s leadership took the necessary steps to ensure that such a tragedy never takes place again.”

The hardest issue debated inside the administration was how to deal with the crown prince himself. Bans against sitting world leaders are rare. A study by administration officials found that the United States had acted against adversaries like President Bashar al-Assad of Syria; Kim Jong-un, the leader of North Korea; President Nicolás Maduro of Venezuela; and Robert Mugabe, the former prime minister of Zimbabwe. But none led countries that were major allies.

“Over all, I’m hugely pleased by the declassification,” said Representative Tom Malinowski, Democrat of New Jersey, who was the assistant secretary of state for human rights in the Obama administration. But he said that a “visa ban for M.B.S. should be mandatory” under existing law “if the secretary of state has credible information that he committed a gross human rights abuse, which the secretary just told us he has.”

Mr. Blinken, Mr. Malinowski said, had the power to waive the visa ban, but only with a report to Congress, with a written justification.

Dennis Ross, a former Middle East negotiator, applauded Mr. Biden for “trying to thread the needle here.”

“This is the classic example of where you have to balance your values and your interests,” Mr. Ross said.

“We are now doing things that show a clear difference from Trump on democracy and human rights,” he added. “On the other hand, there isn’t an issue in the Middle East where we don’t need them to play a role — on Iran, on competing with the Chinese. And if you sanction the crown prince directly you basically create a relationship of hostility, and you force them to show that there is a high price the United States has to pay for that.”

Mr. Biden and his aides have repeatedly said that they intend to take a far tougher line with the Saudis than did President Donald J. Trump, who vetoed legislation passed by both houses of Congress to block weapons sales to Saudi Arabia.

While Congress did not have the votes to override the vetoes, Mr. Biden announced this month that he was banning billions of dollars in arms shipments to Saudi Arabia for its continuing war in Yemen, which he called a “humanitarian and strategic catastrophe.”

The release on Friday of a declassified summary of the American intelligence findings on the Khashoggi killing was also a reversal of Trump administration policies. Mr. Trump refused to make it public, knowing it would fuel the action for sanctions or criminal action against Prince Mohammed.

Human Rights Watch, one of the main advocates for moving human rights issues to the center of American diplomacy, praised the release of the report and said it made “clear that the U.S. needs to act now to put human rights at the forefront of its relationship with Saudi Arabia.” That is exactly what Biden administration officials say their raft of new actions will do.

But the group added that the United States should declare that its freeze on offensive weapons to Saudi Arabia would not be lifted until the Saudis themselves brought those implicated in the killing to justice, “including the crown prince.”