WASHINGTON — A divided federal appeals court panel on Wednesday ordered an immediate end to the case against Michael Flynn, President Donald Trump’s former national security adviser — delivering a major victory to Flynn and to the Justice Department, which had sought to drop the case even though Flynn twice pleaded guilty.

In the ruling, two of three judges on a panel for the Court of Appeals for the District of Columbia ordered the trial judge overseeing the matter, Judge Emmet G. Sullivan, to immediately dismiss the case without further review. The full appeals court has the option of reviewing the matter.

The case is “about whether, after the government has explained why a prosecution is no longer in the public interest, the district judge may prolong the prosecution by appointing an amicus, encouraging public participation, and probing the government’s motives,” wrote Judge Neomi Rao, a former White House official whom Trump appointed to the appeals court last year.

She added: “On that, both the Constitution and cases are clear: He may not.”

The panel ruling raised the question of whether Sullivan, who has a lawyer representing him in the appeals court, will ask the full appeals court to reverse the order — or whether the full court might use a rarely invoked rule that permits it to order a rehearing on its own, without any petition, if the judges deem the matter to involve “a question of exceptional importance.”

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Rao’s decision was joined by Judge Karen L. Henderson, a 1990 appointee of President George Bush. A third judge on the panel, Judge Robert L. Wilkins, a 2014 appointee of President Barack Obama, dissented, saying Sullivan should be permitted to complete his review before deciding whether to grant the government’s motion to dismiss.

The ruling was a surprise because Henderson had asked questions during oral arguments this month that seemed to signal skepticism about short-circuiting Sullivan’s review.

Sullivan had appointed an outsider to critique the motion — John Gleeson, a former federal judge — who argued that the Justice Department’s arguments for dropping the case were baseless and a “pretext” for an illegitimate political intervention on behalf of a presidential favorite, and urged Sullivan to instead sentence Flynn.

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This article was written by Charlie Savage, a reporter for The New York Times.