Ten detainees at Guantanamo have been charged before the tribunals.
The ruling was written by Justice John Paul Stevens.
Stevens said the proposed trials were illegal under U.S. law and the Geneva conventions.
Salim Ahmed Hamdan is a Yemeni who worked as a bodyguard and driver for Usama bin Laden.
Hamdan, 36, has spent four years in the U.S. prison in Cuba.
Hamdan faces a single count of conspiring against U.S. citizens from 1996 to November 2001.
Two years ago, SCOTUS rejected Bush's claim to have the authority to seize and detain terrorism suspects and indefinitely deny them access to courts or lawyers.
In the Hamdan case justices focused solely on the issue of trials for some of the men.
The SCOTUS vote was split 5-3.
Justice Anthony M. Kennedy joined the court's liberal members in ruling against the Bush administration.
Chief Justice John Roberts didn't participate.
As an appeals court judge Roberts had previously backed the U.S. government over Hamdan.