The high court previously allowed construction of the border wall to continue, even after a federal appeals court ruled in June that the administration had illegally sidestepped Congress in transferring the Defense Department funds.
The case will not be argued before the winter and it is unclear how the case will be affected if Democrat challenger Joe Biden defeats Donald Trump in 3 November’s presidential election.
It is also not clear whether the administration has spent all of the $2.5 billion (£1.9bn) it moved to the wall project.
Following an order in July that allowed construction to continue, Justice Stephen Breyer wrote that the court's action “I fear, may operate, in effect, as a final judgement.”
The case has its origins in the 35-day partial government shutdown that started in December 2018.
Mr Trump ended the shutdown after Congress gave him approximately $1.4 bn (£1.07) in border wall funding, far less than the $5.7bn (£4.3bn) he was originally seeking.
The president then declared a national emergency to take cash from other government accounts to use to construct sections of the wall.
At the time, the money Mr Trump identified for the wall included $2.5bn (£1.9bn) in Defense Department money, $3.6bn (£2.7bn) from military construction funds and $600m (£461m) from the Treasury Department’s asset forfeiture fund.
The case before the Supreme Court involved just the $2.5bn in Defense Department funds.
The American Civil Liberties Union sued the Trump administration on behalf of the Sierra Club and Southern Border Communities Coalition, while California led a similar lawsuit on behalf of several states.