"Let us renew our resolve against those who perpetrated this barbaric act and who plot against us still," Obama said at a ceremony at a memorial at the Pentagon military headquarters, which was hit by a hijacked plane.
"In defense of our nation, we will never waver," Obama said on a rainswept day so different from the crisp September morning when Al-Qaeda hijackers showered death and destruction on New York, Washington and Pennsylvania.
"In pursuit of Al-Qaeda and its extremist allies, we will never falter," said Obama, who has taken a strategic decision to escalate the increasingly unpopular war against the Taliban and Al-Qaeda remnants in Afghanistan.
The September 11 attacks, though seven years before Obama was elected, left a legacy that still dominates much of the political environment he must navigate as president.
As well as the long struggle in Afghanistan, the Bush-era foreign policy doctrine ushered in by the attacks led to war in Iraq, legal wrangles over controversial interrogation methods and the "war on terror" camp at Guantanamo Bay, Cuba which Obama has vowed to close.
One of his toughest assignments is Afghanistan, amid rising opposition in Congress to any new troop deployment and with public opinon souring against the war: 57 percent of those asked in a recent CNN poll opposed the conflict.
The president, who opened a day of national ceremonies by observing a moment's silence at the White House, said that "eight Septembers have come and gone" since the attacks, but grief still lingered.
"No turning of the season can diminish the pain and the loss of that day. No passage of time and no dark skies can ever dull the meaning of this moment."
Locked in a fierce partisan struggle with his political opponents on issues like health care, Obama also recalled the unity and common purpose that took over America in the days after the attacks.
"On a day when others sought to sap our confidence, let us renew our common purpose," he said.
"Let us remember how we came together as one nation, as one people, as Americans, united not only in our grief but in our resolve to stand with one another, to stand up for the country we all love."
Obama spoke to a crowd of relatives of the 184 people killed at the Pentagon when a hijacked airliner turned one side of the building into a fireball, and laid a wreath at the memorial.
Earlier, at exactly 8:46 am (1246 GMT) when the first plane piloted by Al-Qaeda hijackers slammed into the north tower of New York's World Trade Center, Obama and First Lady Michelle Obama stood with heads bowed outside the White House.
Ceremonies were also being held in New York, at the Pentagon and in a Pennsylvania field where a fourth plane crashed short of its target.
Obama stepped out in front of the South Portico of the White House, with First Lady Michelle Obama, who was wearing a black dress.
After three chimes played by a US Marine in ceremonial dress, the first couple bowed their heads and observed the moment of silence, joined by around 150 members of the White House staff.
A Marine bugler played then played a haunting rendition of Taps, the military lament played over soldiers' graves.
Above, the huge American flag on top of the White House hung limply at half-mast.
For hours before the ceremony, rain had sluiced Washington, but moments before Obama and the First Lady appeared the rain tapered off and they were able to stand bare-headed.
As soon as they returned to the White House, the deluge resumed.
In a message carried on the front page of the New York Daily News, Obama declared "we are all New Yorkers" and that the attacks "will be forever seared in the consciousness of our nation."
The president wrote that the Afghan war was part of his strategy "to take the fight to the extremists who attacked us on 9/11."
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