America showed its solidarity with heartbroken family members by holding silences at 8.46am and 9.03am, marking the moment the two planes struck.
Among those remembering their loss was Robert Peraza.
His son Rob, a trader with investment bank Cantor Fitzgerald, was killed aged 30.
Touching the spot where his name is engraved at the Ground Zero memorial, head bowed, he said: "Rob, we love you, we are with you all the time and we'll never forget, we'll never forget, we'll never forget."
Relatives were joined by President Barack Obama, first lady Michelle and former leader George W Bush and his wife Laura.
"God is our refuge and strength… We will not fear, even though the Earth be removed, though the mountains be carried in the midst of the sea, " said the president, reading from Psalm 46:2.
Mr Obama and his wife also attended further memorial services at the Pentagon, another target, and in Pennsylvania, where American Airlines Flight 77 went down.
In Britain, Prince Charles comforted those who lost loved ones in the atrocity, and a service was held in London's St Paul's Cathedral.