The justices agreed to review a US appeals court ruling that Salim Ahmed Hamdan, a Yemeni accused of being Osama bin Laden's bodyguard and driver, could be tried by a military tribunal.
The court's decision is seen as a major test of the US government's wartime powers.
The court will hear arguments in the case in the spring, with a decision expected by June.
It will be the first time the court has decided a case involving Bush's War on Terrorism since rulings in June 2004 that rejected the Bush administration's legal position.
The 15 July ruling by the appeals court was made by a three-judge panel that included Judge John Roberts, who was later nominated by Bush for the Supreme Court and who has become the chief justice.
Roberts said in the high court's brief order that he did not take part in considering Hamdan's appeal to the Supreme Court. Roberts told the Senate Judiciary Committee that he would not take part on the Supreme Court in any matter in which he had participated while on the appeals court.
Chief Justice John Roberts with
his family at the Supreme Court
The court's intervention was a surprise. In 2004 justices took the first round of cases stemming from the government's war on terrorism. Justice Sandra Day O'Connor, who is retiring, wrote in one case that "a state of war is not a blank cheque for the president when it comes to the rights of the nation's citizens".
Hamdan's case brought a new issue to the court, the rights of foreigners who have been charged and face a military trial in a type of proceeding resurrected from the second world war.
The trial of Hamdan and three other low-level suspects were interrupted last autumn when a judge in Washington said the proper process had not been followed.
The men are among about 500 foreigners, many swept up in the US-led war in Afghanistan, who have been held at the US military prison in Cuba. The government had planned to proceed with a military trial for another foreigner, Australian David Hicks, with a pre-trial hearing later this month, but that will likely be stalled now.
Guantanamo Bay has become a flashpoint for criticism of the United States overseas and by civil libertarians. Initially, the Bush administration refused to let the men see lawyers or challenge their imprisonment. The high court in 2004 said US courts were open to filings from the men, who had been designated enemy combatants.
Retired military leaders, foreign legislators, historians and other groups had pressed the Supreme Court to review the case of Hamdan, who like many Guantanamo inmates began a hunger strike over the summer.
The military tribunals, formally called military commissions, were authorised by Bush after the 11 September 2001, attacks.
Charges have been referred to a commission for four individuals, including Hamdan.