In a 5-3 ruling, the justices also said the tribunals are illegal under both military justice law and the Geneva Convention, Scotusblog reported.
It was a blow to the Bush administration, which had argued suspects can be held without charges in a military prison without the protections of the U.S. criminal justice system by designating them an enemy combatant.
"The military commission at issue is not expressly authorized by any congressional act," wrote Justice John Paul Stevens for the majority.
The challenge was brought to the high court by lawyers for detainee Salim Ahmed Hamdan, who was al-Qaida leader Osama bin Laden's driver and bodyguard.
The military prison opened in 2002, and still has about 460 men suspected of links to al-Qaida and the Taliban, CNN said.