A federal judge has reluctantly granted a request by the Justice Department to formally dismiss a criminal case accusing five members of the Proud Boys, the far-right group, of seditious conspiracy in connection with the attack on the Capitol on Jan. 6, 2021.

In an order filed on Friday night, the judge, Timothy J. Kelly of Federal District Court in Washington, said that he did not agree with the Trump administration’s decision to dismiss the charges against the Proud Boys — one of the last traces of the Justice Department’s vast investigation of the Capitol attack.

Judge Kelly, who was appointed by President Trump, simply noted that he had little choice but to accept the administration’s move to end the case, especially given Mr. Trump’s sweeping grant of clemency to all of the nearly 1,600 people charged for taking part in the riot.

Acknowledging that his hands were tied, Judge Kelly nonetheless went out of his way to say that the president’s views on Jan. 6 were well known, regardless of whether “those views are based on fact or fiction.” He also took pains to contradict the tide of revisionist history surrounding the riot, writing that what took place at the Capitol was “a perilous event” that was an assault on “the peaceful transfer of power from one president to the next, what President Reagan called ‘nothing less than a miracle.’”

“If this nation’s experiment in self-government is to last another 250 years, the American people — no matter their partisan preferences — will have to act together to preserve, protect and defend that miracle through our constitutional framework,” Judge Kelly added.

The dismissal of the case against the Proud Boys — all of whom were sentenced to significant prison terms before Mr. Trump pardoned them or commuted their sentences — was a largely symbolic move. But it represented an important moment in the broader story of the Justice Department’s inquiry into Jan. 6, bringing an end to one of the investigation’s most important cases.

The Proud Boys played an instrumental role in the violence and chaos that erupted that day in 2021 at the Capitol, taking part in several breaches of police lines and helping to instigate the mob to storm the building. One of the defendants in the newly dismissed case, Dominic Pezzola, was captured in a searing image shattering a window at the Capitol with a stolen police riot shield, creating, as Judge Kelly wrote, “the first entry point through which hundreds of rioters streamed into the building.”

Federal prosecutors first requested that the case be closed in May, saying that dismissing the charges was “in the interests of justice.” At the same time, they asked for the dismissal of cases against a dozen members of another far-right group, the Oath Keepers militia, who had also been charged with seditious conspiracy.

Most of the Proud Boys and Oath Keepers charged in those cases had not received full pardons, but rather had their sentences commuted — a move that freed them from prison. The judge overseeing the Oath Keepers cases, Amit P. Mehta, also of the U.S. District Court in Washington, has not yet joined Judge Kelly in issuing a ruling dismissing them.

Enrique Tarrio, the leader of the Proud Boys who was sentenced to 22 years in prison before he was pardoned, praised the dismissal in a social media post on Friday night.

“Tonight we celebrate,” he wrote, adding that he and his four co-defendants would press forward with a lawsuit they had filed accusing the Justice Department of malicious prosecution.

“We continue this fight in civil court,” Mr. Tarrio wrote. “We hold the bastards who did this accountable.”