The US president's refusal to reject preventive detention was the reason al-Marri's lawyers had pushed the case in the Supreme Court even though al-Marri now faces a civilian trial, not a military one.
However the judges did dismiss an earlier federal appeals court ruling al-Marri was challenging, which had affirmed the president's power to detain people in the US without trial.
Jonathan Hafetz, a lawyer for the American Civil Liberties Union (ACLU) lawyer who represents al-Marri, told the Associated Press news agency he would have preferred a court ruling that settled the issue once and for all.
However, he said he was pleased the court did not let the appeals court ruling stand.
"We trust that the Obama administration will not repeat the abuses of the Bush administration having now chosen to prosecute Mr. al-Marri in federal court rather than defend the Bush administration's actions in this case," he said.
Al-Marri had been designated an enemy combatant by the Bush administration, which argued that he could be held indefinitely without being charged.
In one of his first acts after taking office last month, Obama ordered US government lawyers to review al-Marri's case.
Al-Marri was arrested in late 2001 as part of the US Federal Bureau of Investigation's probe into the September 11 attacks.
Prosecutors initially indicted him on charges of credit card fraud and lying to the FBI, although al-Marri also denied those charges.
In June 2003, Bush said al-Marri had vital information about potential attacks, declared him an enemy combatant and ordered him transferred to military custody.