President Barack Obama laid a wreath at the memorial where each of the 184 victims of the attack there is remembered with a bench and a small reflecting pool. The benches with the names of victims from the Pentagon face the building. The markers of the victims aboard the plane face out to the sky.
A military band played "Amazing Grace" as the president greeted visitors to the memorial.
Vice president Joe Biden paid tribute to what he called the "9/11 generation" of American service members. He told the 1,600 people at the ceremony that "Hope can grow from tragedy."
"Never before in our history has America asked so much over such a sustained period of an all-volunteer force," Biden said. "So I can say without fear of contradiction or being accused of exaggeration, the 9/11 generation ranks among the greatest our nation has ever produced, and it was born - it was born - it was born right here on 9/11."
Secretary of Defense Leon Panetta and Chairman of the Joint Chief of Staff Admiral Mike Mullen were also at the site to honor the victims.
"At this very moment on this very spot, it is difficult to believe that 10 years ago this was the scene of incredible devastation, at this spot, at this very moment," Panetta said.
"They could bring down the walls, but they could not bring down America," Mullen said. "They could kill our citizens, but they could not kill our citizenship."
Panetta paid tribute to 6,200 members of the U.S. military who have died in the Iraq and Afghan wars.
"These past 10 years tell a story of resilience," Obama said at a memorial concert at the Kennedy Center after he visited all three attack sites.
"It will be said of us that we kept that faith; that we took a painful blow, and emerged stronger," he said. The Associated Press contributed to this report.