The decision means the court will not rule on the constitutionality of an anti-terror law pushed through Congress by President George W Bush last year.
The provision in question states that Guantanamo Bay inmates cannot challenge their detention in US civil courts.
Many of the 385 detainees at the camp have been held for five years or more.
None has yet been able to challenge their detention in a US civil court.
The provision stripping detainees of their right to mount a legal challenge to their confinement was upheld by a federal appeals court in Washington in February.
The court's majority opinion was that "the will of Congress" should prevail and that habeas corpus did not apply to foreign nationals being held at Guantanamo Bay because it is not US soil.
The detainees have argued that they are entitled to access to US courts wherever they are being detained by the US authorities.
Military tribunals
Observers say the latest Supreme Court judgement is unlikely to be its final say on the issue.
Three of the nine Supreme Court justices - Stephen Breyer, David Souter and Ruth Bader Ginsburg - dissented from the majority ruling.
"I believe these questions deserve this court's immediate attention," Justice Breyer wrote.
Two others said they were rejecting the appeals only on procedural grounds.
The Supreme Court in 2004 and 2006 opposed the Bush administration's position on the legal rights of Guantanamo bay prisoners.
Pushing the anti-terror legislation through Congress last year, Mr Bush said he needed the new law to bring terror suspects to justice.
It allows for the indefinite detention of people as "enemy combatants".
Last week, Australian David Hicks became the first inmate to have his case heard by a special Guantanamo Bay military tribunal.
He is the first Guantanamo detainee convicted of any terrorist offence since the camp was set up a little over five years ago.
The US has said it plans to use the military tribunal system to prosecute about 80 of 385 prisoners remaining at the camp.
