Former first lady Laura Bush joined Obama in rural western Pennsylvania, marking a rare joint public speaking appearance by two first ladies. Obama thanked her predecessor for helping the country through the difficult days following the attacks.
"May the memory of those who gave their lives here continue to be an inspiration to you and an inspiration to all of America," Obama said to the thousands gathered for the annual service.
The crowd filled a temporary memorial just west of the crash site, many toting American flags or bunches of flowers.
"It was clear that these 40 individuals were no strangers to sacrifice," Obama told the crowd, citing the presence of veterans, coaches and volunteers among them.
"Being a hero is not just a matter of faith, it's a matter of choice."
Future generations would come to the site, she said, to "see how a scar in the earth has healed."
"It is truly my prayer today that all who come here will be filled with hope," she said.
Obama and Bush met privately with the victims' families before the service. Obama greeted each one with a hug and her condolences. Bush told the crowd that "Americans have no division" on this day.
"Nine years ago, in this skies above this field and in Washington and in New York City, we saw the worst of our enemy and the best of our nation," she said. "In the face of terror, Americans chose to overcome evil."
Former President George W. Bush issued a statement Saturday saying he and his wife were thinking of and praying for the 9/11 victims and their families.
"On September 11, 2001, Americans awoke to evil on our shores," he said. "We recall the many acts of heroism on that day, and we honor those who work tirelessly to prevent another attack."
A moment of silence at the service near Shanksville, Pa., was broken with relatives reading aloud the names of the 40 passengers and crew who died and a bell tolling for each one.
Flight 93 was en route from Newark, N.J., to San Francisco on Sept. 11, 2001, when hijackers seized control. But passengers fought back and the hijackers responded by crashing the plane about 60 miles southwest of Pittsburgh.
The service was at a temporary memorial near the crash site. A permanent memorial is under construction, and completion of the first phase is expected by next year's anniversary.
Gerald Bingham, 67, of Churchill, Tenn., who lost his son, Mark, in the crash, said it meant a lot to him to have both Obama and Bush there. He said it was important that people remember the victims and support efforts to build the memorial.
"This is a story that needs to be told," Bingham said. "It's something we can all take a lesson from what they did on that plane."
Asked about the controversies over construction of a mosque near ground zero in New York City, and over a Florida pastor's now-canceled plans to burn copies of the Quran to mark the Sept. 11 anniversary, Bingham said he had no time to worry about such things.
"We're trying to move forward here," he said.