The presidents and their wives stood behind bulletproof glass during the ceremony, an indication of the tight security surrounding the day's events. In Washington, Obama's chief counterterrorism adviser convened a meeting in the Situation Room to review security threats.
Obama's stop in Shanksville drew spontaneous applause and chants of "USA" from those at the memorial site. Obama and his wife lingered at the site to pose for photos with visitors, greet children and share some laughs.
His mood seemed to brighten the longer he went.
"Thanks for getting bin Laden," one man called out, referring to the Sept. 11 mastermind tracked down and killed in Pakistan earlier this year.
The Obamas walked to a boulder that marks the actual crash site and stood quietly together in a field of wildflowers for a time.
"I think it's just important that the president shows his support for the families that lost loved ones," said Jaleel Dyson, an 18-year-old from Washington who attends college in the area and came to pay tribute to the dead.
At the Pentagon, the Obamas took their time mingling with memorial visitors and victims' family members, some of them wearing ribbons and T-shirts bearing the names and photos of their loved ones. Here, too, amid the sadness, there were smiles and laughter.
Obama, who was an unknown state senator from Illinois when the hijackers struck, has called on Americans to remember and serve — and to come together.
"Ten years later, I'd say America came through this thing in a way that was consistent with our character," he told NBC News. "We've made mistakes. Some things haven't happened as quickly as they needed to. But overall, we took the fight to al-Qaida, we preserved our values, we preserved our character."
In the broadcast interview, Obama recalled going home after the attacks and rocking his baby daughter, Sasha. "Our first reaction was, and continues to be, just heartbreak for the families involved. The other thing that we all remember is how America came together."
Capping a journey of heavy emotion, Obama said in the nighttime event in Washington that the legacy of 9/11 will be that the country took an enormous blow and emerged stronger. He said the Americans will remember that when they visit the memorials for decades to come.
"They will know that nothing can break the will of a truly United States of America," he said. "They will remember that we have overcome slavery and Civil War; we've overcome bread lines and fascism, recession and riots, Communism and, yes, terrorism."
Associated Press writers Darlene Superville, Erica Werner and Stacy Anderson contributed to this story.