While Obama made no direct mention of the crisis in Syria, he vowed to "defend our nation" against the threats that endure, even though they may be different than the ones facing the country during the 2001 attacks.
"Let us have the wisdom to know that while force is sometimes necessary, force alone cannot build the world we seek," Obama said during a ceremony at the Pentagon.
The president spoke the morning after an address to the nation where he defended a possible military strike on Syria in retaliation for a deadly chemical weapons attack. But he expressed some hope that a diplomatic solution might emerge that would keep the U.S. from having to launch a strike. In the afternoon he volunteered at a Washington charity, urging Americans to also observe the day by helping their communities.
Among those gathered at the Pentagon Wednesday where family members of those killed on Sept. 11, 2001. Many wore red, white, and blue striped ribbons and some cried as the president spoke.
"Our hearts still ache for the futures snatched away, the lives that might have been," Obama said.
The morning was sunny as it was a dozen years ago at the time of the attack, but the temperature was hotter and climbing toward a high in the 90s. A few in the crowd were treated for effects of the heat by military medics, and the president wiped his face with a handkerchief as he spoke.
The president also paid tribute to the four Americans killed one year ago in an attack on a U.S. compound in Benghazi, Libya, asking the country to pray for those who "serve in dangerous posts" even after more than a decade of war.
In a commemorative event at the Justice Department, Attorney General Eric Holder called on an audience of several hundred employees to remember "the nearly 3,000 innocent people whose lives were lost" and to pay tribute to the 72 law enforcement officers who were killed trying to save others.
Obama opened the day with a somber remembrance at the White House. The searing memory of death and destruction brought him to the South Lawn for a moment of silence and reflection a dozen years after terrorists emblazoned this date indelibly in people's minds, hearts and calendars as "9/11."
Along with first lady Michelle Obama, Vice President Joe Biden and wife Jill Biden, the president walked out of the White House to the lawn at 8:46 a.m., EDT - the moment on Sept. 11, 2001, when the first plane hit the World Trade Center tower in New York.
Obama and staff assembled there with him bowed their heads to observe a moment of silence, and then listened as a bugler played "Taps."
Later Obama visited Food & Friends, a Washington charity that delivers meals to people with HIV/AIDS, cancer and other life-threatening illnesses. He donned an apron and a baseball cap with the charity's logo and packed apples, bananas and pre-wrapped sandwiches as part of a volunteer assembly line.
Obamas said Sept. 11 is an occasion not just to remember the victims of the terrorist attack, but for "neighbors helping neighbors."
He encouraged Americans to "look for a way to volunteer in your own community."