A minute's silence has been observed for the victims of the September 11 attacks on the World Trade Center.
The remembrance service comes three months to the day after the two airliners slammed into the Twin Towers.
The US national anthem was played in the presence of outgoing New York mayor Rudi Giuliani.
President George Bush commended the courage of rescue workers and the outpour of sympathy from nations around the world.
He said: "Today justice is being done. We still have far to go yet there can be no doubt how this conflict will end.
"This country is young, but its memory is long. It is a memory of tragedy, loss and mourning, but a memory also of bravery and self-sacrifice."
He thanked the families of Flight 93 - the flight that crashed in Pennsylvania - for the courage of their relatives "who may have saved the White House".
Tanaiste Mary Harney visited Ground Zero yesterday and is due to fly back to Ireland later today.