President Barack Obama and First Lady Michelle Obama wrapped up their observance of the 11th anniversary at Arlington National Cemetery.
They visited the graves of military members killed in Iraq and Afghanistan.
Obama left presidential challenge coins, which honor achievement, at the headstones.
The Obamas also paid tribute to the 184 people killed at the Pentagon.
Aided by a Marine honor guard, the president laid a white floral wreath on a concrete slab inscribed with the date and time of the attack.
"I've always said that our fight is with Al Qaeda and its affiliates, not with Islam or any other religion," Obama said. "This country was built as beacon of freedom and tolerance. That's what's made us strong, now and forever."
The Obamas also observed a moment of silence at the White House.