The Supreme Court on Wednesday rejected President Trump’s emergency request to freeze nearly $2 billion in foreign aid in a closely divided decision indicating that the justices will subject his efforts to reshape the government to close scrutiny.

The court’s brief order was unsigned, which is typical when the justices act on emergency applications. It said only that the trial judge, who had ordered the government to resume payments, “should clarify what obligations the government must fulfill.”

But the ruling represented one of the court’s first moves in response to the flurry of litigation filed in response to Mr. Trump’s efforts to slash government spending and take complete control of the executive branch. The vote was 5 to 4, with Chief Justice John G. Roberts Jr. and Justice Amy Coney Barrett joining the three liberal members to form a majority.

Although the language of the order was mild, tentative and not a little confusing, its bottom line was that a bare majority of the court ruled against Mr. Trump on one of his signature projects. The president’s plans to remake American government, the order indicated, will have to face a court more skeptical than its composition, with six Republican appointees, might suggest.

That, in turn, is likely to give rise to major rulings testing and perhaps recalibrating the separation of powers required by the Constitution.

Justice Samuel A. Alito Jr., writing for the four dissenting justices, said the majority had gone profoundly astray.