In a bitterly divided 5-4 decision, the court said the administration must give Venezuelans who it claims are gang members "reasonable time" to go to court.
But the conservative majority said the legal challenges must take place in Texas, instead of a Washington courtroom.
In dissent, the three liberal justices said the administration has sought to avoid judicial review in this case and the court "now rewards the government for its behavior." Justice Amy Coney Barrett joined portions of the dissent.
The justices acted on the administration's emergency appeal after the federal appeals court in Washington left in place an order temporarily prohibiting deportations of the migrants accused of being gang members under the rarely used Alien Enemies Act.
The case has become a flashpoint amid escalating tension between the White House and the federal courts.