Granting a request by federal prosecutors, the judge overseeing former President Donald J. Trump’s classified documents case ordered his lawyers on Tuesday to redact the names of about two dozen government witnesses from a public version of one of their court filings to protect them against potential threats or harassment.

In a 24-page ruling, the judge, Aileen M. Cannon, told Mr. Trump’s lawyers to refer to the witnesses in their filing with a pseudonym or a categorical description — say, John Smith or F.B.I. Agent 1 — rather than identifying them by name.

The special counsel, Jack Smith, had expressed a deep concern over witness safety, an issue that has touched on several of Mr. Trump’s criminal cases. Among the people prosecutors were seeking to protect were “career civil servants and former close advisers” to Mr. Trump, including one who had told them that he was so concerned about potential threats from “Trump world” that he refused to permit investigators to record an interview with him.

Judge Cannon’s decision, reversing her initial ruling on the matter, was noteworthy, if only for the way it hewed to standard practice. After making a series of unorthodox rulings and allowing the case to become bogged down by a logjam of unresolved legal issues, the judge has come under intense scrutiny. Each of her decisions has been studied closely by legal experts for any indication of how she plans to proceed with other matters.

But as she has in other rulings where she found in favor of Mr. Smith, Judge Cannon used her decision on Tuesday to take a shot at the special counsel, with whom she has been feuding. Although she agreed with him, she pointed out that his request to protect “all potential government witnesses without differentiation” was “sweeping in nature” and that she was “unable to locate another high-profile case” in which a judge had issued a similar decision.

The fight over the witnesses began in earnest in early February when Mr. Smith’s prosecutors asked Judge Cannon to reconsider a decision she had made allowing Mr. Trump to publicly name about 24 witnesses in court papers they had filed asking the government for additional discovery information.

The prosecutors told Judge Cannon they could not fathom why the lawyers needed to identify any of the witnesses as part of their request for more information. Mr. Trump’s legal team has argued that it has a free speech right to name the witnesses, but Mr. Smith’s deputies have scoffed at that contention.

“This is not about Donald Trump vindicating the First Amendment,” one of the prosecutors, David Harbach, said at a hearing in the case last month. “It’s just not. And we have to call it out for what it is.”

The prosecutors also told Judge Cannon that if she refused to reverse her initial ruling allowing Mr. Trump to release the names, they would challenge her decision in front of an appeals court. They were willing to directly confront her because, they said, if the witnesses were publicly identified they would be exposed to “intolerable and needless risks.”

“There is a well-documented pattern in which judges, agents, prosecutors and witnesses involved in cases involving Trump have been subject to threats, harassment and intimidation,” the prosecutors wrote.

Judges in two of the former president’s other cases — one in Washington and another in Manhattan that is set to go to trial next week — have imposed gag orders on him specifically to protect witnesses from his attacks.