Bush and Vice President Dick Cheney answered questions from the commissioners for more than three hours.
The president dismissed suggestions that he appeared before the panel with Cheney to coordinate stories.
"If we had something to hide, we wouldn't have met with them in the first place," Bush said. "We answered all their questions."
Bush said it was important for him and Cheney to appear together so that commission members could "see our body language... how we work together."
Bush described the session as "cordial," but declined to provide any details about topics discussed. He said he was never advised by White House Counsel Alberto Gonzales -- who attended the session, along with two members of his staff -- not to answer a question.
Bush stressed that the United States remains vulnerable to terrorist attacks.
"So long as there's an al Qaeda enemy that's willing to kill, we are vulnerable," Bush said.
A statement from the 9/11 commission described the meeting as "extraordinary" and thanked the two men for their cooperation.
"The commission found the president and the vice president forthcoming and candid," the statement said. "The information they provided will be of great assistance to the commission as it completes its final report."
Commission member Tim Roemer, a Democrat and former congressman from Indiana, said Bush was "very direct" in his answers.
"He was cooperative, he was frank, he was gracious with his time," Roemer told CNN.
The commission is investigating what has become the defining moment of the Bush presidency -- the worst terrorist attacks on U.S. soil, carried out by 19 hijackers who commandeered four U.S. commercial jets.
Two of those jets slammed into New York's World Trade Center, causing the towers to collapse, a third jet crashed into the Pentagon, and the fourth slammed into a field in western Pennsylvania. About 3,000 people were killed.
