In New York, somber string music played at Ground Zero, where families read the names and held up photos of those who were killed when two hijacked airliners smashed into the World Trade Center Twin Towers.
Family members of victims of the 2001 and 1993 attacks on the World Trade Center were invited to read names of the victims at Wednesday's observance. The 1993 Trade Center bombing killed six people.
Plans called for the Tribute in Light -- twin beams of light to honor first responders and others -- to be turned on at sunset and turned off at dawn Thursday, the New York Post said.
In Washington, President Barack Obama, first lady Michelle Obama, Vice President Joe Biden and his wife, Jill Biden, observed a moment of silence on the South Lawn of the White House along with White House staffers.
Following a wreath-laying ceremony at the Pentagon, the president told survivors and families of the victims, "In your resilience, you've taught us all there is no trouble we cannot endure [and] no calamity we cannot overcome."
He also paid tribute to the four Americans who died Sept. 11, 2012, in the terrorist attack on the U.S. Consulate in Benghazi, Libya, including U.S. Ambassador to Libya Christopher Stevens.
Following Obama's remarks, a military band played "America the Beautiful" and "Amazing Grace."
Bells tolled as the names of the passengers and crew of United Flight 93 were read at the Shanksville site, which has been named a national memorial.
Secretary of the Interior Sally Jewell joined Flight 93 Memorial Superintendent Jeff Reinbold, Flight 93 Families President Gordon Felt and National Park Service employees -- along with volunteers and families -- for the memorial in Shanksville.
"This memorial we are surrounded by today protects and honors the remains of these heroes and ensures that generations from now, the story of Flight 93 will still remind and inspire those who come after us," Jewell said. "It is a testament to the 40 that 300,000 people a year visit this place of honor and more than 100,000 people have donated to build the memorial."
White House spokesman Jay Carney told reporters at Wednesday's daily briefing the president would participate in a national day of service and remembrance event, while the first lady would visit with military families at a USO Warrior and Family Center at Fort Belvoir, Va., joining children of military personnel in making patriotic-themed crafts.
The Bidens are to host a barbecue at the Naval Observatory in Washington for wounded warriors and their families.
On Sept. 11, 2001, 19 terrorists hijacked four commercial airplanes. Two were flown into the World Trade Center's Twin Towers in New York City, one plowed into the Pentagon in Washington and the fourth crashed in a field near Shanksville.
The death toll: 2,753 people in the Twin Tower attacks, including 343 firefighters, 23 New York police officers and 37 Port Authority officer; 184 people at the Pentagon; and 40 passengers and flight crew members of the plane that crashed in Pennsylvania. The passengers and crew stormed the hijacked plane's cockpit, foiling the hijackers' plans to fly the plane into an unknown target.
In New York, Bruni Sandoval told The New York Times she attends the observance annually to remember her friend, Nereida De Jesus.
"It helps a little," she said.
Families gathered between the reflecting pools, placing roses and other mementos on the names of the dead as bagpipes sounded through the streets of Manhattan before the ceremony began.
The ceremony was the last over which Mayor Michael R. Bloomberg presided. A new mayor will be elected Nov. 5.
New York Gov. Andrew Cuomo arrived at the ceremony riding a Harley-Davidson motorcycle along with musician Billy Joel, firefighters and others participating in a tribute ride from a firehouse to Ground Zero.
Other remembrances were held in cities across the country.
In one, 90 miles north of Ground Zero, below the Hudson River flight path hijacked American Airlines Flight 11 and United Airlines Flight 175 took as they made their way south to the World Trade Center, Mayor Shayne Gallo of Kingston, N.Y., observed that on Sept. 10, 2001, Americans lived their lives generally indifferent to each other and feeling separated by their differences.
"It's sadly ironic that it takes horrific events to put things into perspective," he said.