With the three liberal justices in dissent, the court said the administration likely violated federal law in its efforts to rescind the program informally known as Remain in Mexico.
A federal judge in Texas had previously ordered that the program be reinstated last week. Both he and the 5th U.S. Circuit Court of Appeals refused the administration's request to put the ruling on hold.
Justice Samuel Alito ordered a brief delay to allow the full court time to consider the administration's appeal.