In a speech at the Pentagon on Thursday, one of the sites of the attacks, the president did not overlook the fact that, besides the more than 3,000 deaths in the attacks undertaken by Al Qaeda using four passenger jets, in the wars launched as a result of that tragedy, more than 6,800 Americans have died.
"Over more than a decade of war, this 9/11 Generation has answered our country's call, and three months from now, our combat mission in Afghanistan will come to an end," Obama emphasised.
Despite having insisted that the US cannot be permanently involved in wars in the Middle East, the president went on national television Wednesday night to explain to Americans why new military interventions in the region must be undertaken.
After having weakened Al Qaeda and killing the group's leader, Osama bin Laden, Obama said that Islamic radicalism once again has become a threat, this time due to the advances of the Islamic State in Syria and Iraq.
But Thursday, Obama focused his speech on the victory of the US people over the hatred and fear of terrorist violence 13 years after the 9/11 attacks.
The terrorists "sought to do more than bring down buildings or murder our people".
"They sought to break our spirit and to prove to the world that their power to destroy was greater than our power to persevere and to build," the president said.
"But you, and America, proved them wrong," he said, addressing survivors and the families of those who died at the Pentagon.
"Thirteen years after small and hateful minds conspired to break us, America stands tall and America stands proud. And guided by the values that sustain us, we will only grow stronger," Obama said.
"Generations from now, no matter the trial, no matter the challenge, America will always be America," he said.
Thursday's largest 9/11 commemoration was in New York, where two of the hijacked airlines destroyed the twin towers of the World Trade Centre.
A ceremony was also held in Shanksville, Pennsylvania, at the spot where the fourth plane crashed amid a struggle between the hijackers and the passengers.