This, in effect, sidesteps a challenge to Bush administration wartime detention powers.
By a 6-3 vote, the court refused to hear an appeal by Jose Padilla, who was confined in a military jail in South Carolina for more than three years after Bush designated him an "enemy combatant".
The US government argued that the appeal over his indefinite detention was now pointless.
Three justices said the court should have agreed to take up the case anyway: Justices David H Souter, Ruth Bader Ginsburg and Stephen Breyer.
Ginsburg wrote to explain why the case should be heard.
"Nothing the government has yet done purports to retract the assertion of executive power Padilla protests. Although the government has recently lodged charges against Padilla in a civilian court, nothing prevents the executive from returning to the road it earlier constructed and defended," she said.
The court's decision does not necessarily mean it agrees with the White House's policy on the detention of "enemy combatants" but it does not go against it and leaves the issue in limbo for now. It can take up Padilla's case again.
Jose Padilla has been held for
over three years without charge
An appeals court panel had all but called for the court to deal with the case, saying it was troubled by the Bush administration's change in legal strategy - after holding Padilla more than three years without charge.
Justices first considered in 2004 whether Padilla's constitutional rights were violated when he was detained as an "enemy combatant" without charge and access to a lawyer.
The justices dodged a decision on technical grounds at the time.
In a dissenting opinion, Justice John Paul Stevens said then that "at stake in this case is nothing less than the essence of a free society".
Stevens and two other court members, Chief Justice John Roberts and Justice Anthony M Kennedy, explained their votes on Monday not to deal with Padilla's case.
Although Padilla's claims "raise fundamental issues respecting the separation of powers, including consideration of the role and function of the courts, [the case] also counsels against addressing those claims when the course of legal proceedings has made them, at least for now, hypothetical", Kennedy wrote for the three.
The court was asked to clarify how far the government can go when its hunt for "terrorists" leads to Americans in the US.
Padilla was arrested in Chicago in 2002 for allegedly plotting to detonate a "dirty bomb".
He was held in a military jail for three years with no access to a lawyer until the US government, under pressure from the courts, finally allowed it.
The US Court of Appeals rejected Padilla's argument that his detention without trial was unconstitutional.
As Padilla's lawyers pursued his case to the Supreme Court, the Bush administration decided to charge him with conspiring to send money abroad for violent reasons rather than with the original "dirty bomber" charge.
The government then moved him to a federal prison in Miami and asked the Supreme Court to declare the case moot.