Sombre ceremonies of remembrance were held on Thursday in New York and Washington, against the backdrop of Obama's pledge to "destroy" Islamic State fighters in Iraq and Syria, a new front in the war on radical Islam.
"As Americans, we draw strength from you, for your love is the ultimate rebuke to the hatred of those who attacked us that bright, blue morning," Obama said to relatives of victims at the Pentagon, scene of one of the 9/11 strikes.
"You've kept alive a love that no act of terror can ever extinguish," he said.
"We carry on because as Americans, we do not give in to fear. Ever."
Obama, his wife Michelle and Vice President Joe Biden earlier observed a moment of silence on the White House south lawn, along with about 300 staffers, with flags in Washington flying at half-mast.
In New York, relatives of those killed when hijacked airliners slammed into the World Trade Centre gathered at Ground Zero to remember the dead.
The ceremony began, as usual, with a moment of silence at 8.46am local time (2246 AEST), when the first plane smashed into the Twin Towers.
Family members then began the long process of reading the names of the nearly 3000 people who were killed in the attacks on New York, the Pentagon and in Shanksville, Pennsylvania.
Several other moments of silence will be observed throughout the day in the Big Apple, including two to mark the times when the towers collapsed, while it's the first year that the 9/11 museum in New York will be open on the anniversary of the attacks.
At the Pentagon, Obama honoured the more than 6800 troops who have lost their lives in Afghanistan and Iraq since 2001, noting that US forces would be wrapping up their combat mission in Afghanistan by the end of the year.
"Today, we honour all who have made the ultimate sacrifice these 13 years," he said, after laying a wreath at the spot where American Airlines Flight 77 crashed into the Pentagon.
"We give thanks to those who served in harm's way to keep our country safe and meet the threats of our time."
While most American troops are due to depart Afghanistan in December, Obama on Wednesday announced the dispatch of another 475 military personnel to help train Iraqi forces to take on Islamic State extremists, bringing the total number of US troops in the country to 1600.
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