The court said it would examine the legality of the military tribunals in early 2006, although the US Defence Department said it still wanted to start the first trial this month of accused "Australian Taliban" David Hicks.
"We're assessing the decision of the Supreme Court," Pentagon spokesman, Bryan Whitman, said.
Mr Whitman said he was unaware of any plan to postpone Mr Hicks' trial.
The Supreme Court challenge was launched by lawyers for Salim Ahmed Hamdan, a Yemeni who like Mr Hicks has been held at the controversial camp at Guantanamo Bay, Cuba since 2002.
Mr Hamdan and Mr Hicks were first detained in Afghanistan in late 2001.
Mr Hamdan has been charged with conspiracy to stage attacks on civilians, murder and terrorism. He has denied the charges.
Nine inmates
He is one of nine inmates to have had preliminary hearings before the special military tribunals at Guantanamo, which have been widely criticised by human rights groups, though the US government has insisted they are fair and legal.
The Pentagon announced terrorism-related charges on Monday against five more detainees at Guantanamo Bay, Cuba.
Conspiracy charges were lodged against Bhassan Abdullah al Sharbi and Jabrain Said bin al Qahtani of Saudi Arabia; Sufyian Barhoumi of Algeria; Binyman Ahmed Muhammad of Ethiopia; and Omar Ahmed Khadr of Canada, the Pentagon said.
However a federal court rule in November last year that the military commissions would violate Mr Hamdan's rights and that he should not be tried until a proper body had decided whether he was a prisoner-of-war.
But a US appeals court ruled on July 15 that the military trials were legal.
The three-judge court included John Roberts, who was recently appointed the Supreme Court's new chief justice.
The July ruling was seen as a victory for President George W Bush's administration and its treatment of detainees from the US war on terrorism.
The Appeals Court said that the 1949 Geneva Convention on prisoner of war rights did not apply to Mr Hamdan and that the US Congress had authorised the military commission.
Due to his role in the appeals court decision, Judge Roberts will have to disqualify himself from Mr Hamdan's Supreme Court hearing, leaving the decision to eight of the nine judges.
Eugene Fidell, a jurist and member of the National Institute of Military
Justice, said the court's decision to have a hearing will likely cause the suspension of the military trials of other detainees, including Mr Hicks.
Mr Hicks, whose trial is due to start on November 18, is accused of fighting alongside the Taliban against US-led forces who invaded after the September 11, 2001 attacks on the United States.
Hicks lawyer
Meanwhile David Hicks' lawyers say his scheduled hearing before a US military commission would be "clearly wrong" given the Supreme Court’s decision to investigate the legitimacy of the process.
The 30-year-old Australian had been due in the next 30 days to face a commission on charges of conspiracy to commit terrorism, attempted murder as an illegal combatant and aiding the enemy, all related to his alleged fighting alongside the Taliban in Afghanistan.
"Four justices of the Supreme Court think there are serious questions about the military commission," Mr Hicks' British lawyer Stephen Grosz said.
"That's encouraging and it would be clearly wrong for David's case to go ahead until the Supreme Court rules on that."
His lawyers in America were expected to immediately apply for a re-institution of a stay of proceedings until the current assessment of the process was completed.
A ruling on Mr Hicks' application for British citizenship was expected by close of business on Wednesday, with his lawyers lodging papers with the High Court for a judicial review should that ruling not be forthcoming.
The Muslim covert from Adelaide, Australia is facing charges of attempted murder and aiding the enemy after allegedly training at Al-Qaeda-linked military camps.
Mr Fidell, a critic of the procedures put in place by the Bush administration, welcomed the court's decision to take the case.
"It's important to take it now," he told AFP. "Almost regardless to how it comes out, it's important to send a message around the world that the issues presented in this case are very important and they are getting attention at the highest level of our governmental system, including the courts."
Fifteen detainees at Guantanamo have now been designated for military commission trials.
Four have been formally charged, including Mr Hamdan, Mr Hicks,
another Yemeni and a Sudanese man.
Around 500 detainees are held at the US military detention facility, which was set up in 2002 soon after the start of the US-led offensive against the Taliban regime in Afghanistan in the fall of 2001.