The White House did not immediately comment on the decision.
About 30% of voters, mostly Democrats, cast postal ballots in the general election two years ago.
Since returning to the White House, Trump has sought to restrict voting by mail. While he himself has voted by post, he has long claimed this method allows non-citizens to cast ballots and is prone to fraud.
In March's executive order, the president directed USPS to introduce unique barcodes on postal ballot envelopes.
State and local election officials would also be required to supply information to an online portal about voters who receive mail ballots.
Twenty-three states and Washington DC sued to stop Trump's order.
The postal workers' union also said clerks could not be trained in time for the election.
In court filings, the Trump administration maintained the new USPS rules were constitutional.
It said states "cannot choose to use the federal mails to carry out their elections but then insist that their election-related mail is somehow exempt from the Postal Service's rule-making authority, conferred by Congress".
Boston-based Judge Indira Talwani imposed an injunction on 4 September blocking Trump's order. She ruled that implementing the measures close to November's elections could disenfranchise voters.
Last week, a US appeals court refused to put Judge Talwani's order on hold.
On Sunday, another federal judge, Judge Carl Nichols, ruled against Trump's order.
Some states have already begun distributing mail-in ballots ahead of the midterm elections, which will decide which party controls Congress.
It is not the first setback on postal ballots for Trump before the Supreme Court.
In June, the justices ruled that states may count ballots postmarked by election day, rejecting the Trump administration's push to block votes being tallied when they are received after polls close.
Trump has previously made false claims that he lost the 2020 election owing to widespread electoral fraud.

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