The observance, along with another at Ground Zero in New York, was held at 8:46 am (1246 GMT), the moment the World Trade Center in Manhattan was struck.
The observance, along with another at Ground Zero in New York, was held at 8:46 am (1246 GMT), the moment the World Trade Center in Manhattan was struck by the first of two hijacked airliners.
The president, and his wife, Melania, placed their hands on their hearts and bowed their heads as a bell tolled and a Marine played the mournful Taps on a trumpet.
In all, four planes were hijacked by Al-Qaeda militants who used them to topple the trade center's twin towers and hit the Pentagon. The fourth plane crashed in a field in Pennsylvania.
The attacks, the deadliest ever on US soil, killed 2,997 people, and plunged the United States into a chain of rolling wars against Islamic militants.
Memorial ceremonies were also being held in New York and at the Pentagon and Vice President Mike Pence was to deliver remarks in Shanksville, Pennsylvania, where the fourth plane crashed.
Pence was also scheduled to tour the Flight 93 National Memorial Visitors Center and take part in a wreath-laying ceremony.