Honouring the dead at Ground Zero
At 0846 local time, the exact time the first plane hit the World Trade Center, the American national anthem rang out at the site, at the White House and across the United States.
More than 80 countries that lost citizens in the attacks answered Mr Bush's call and held their own ceremonies to commemorate the estimated 3,900 people who died.
US embassy staff in Tokyo and Japanese officials were among the first on Tuesday morning to commemorate the victims of the deadly suicide strikes.
Prime Minister Junichiro Koizumi released a statement, underlining his pledge to fight international terrorism and provide support for the reconstruction of Afghanistan.
In Australia, diplomats gathered at the residence of the American ambassador and mourned the deaths by planting a symbol of life: an oak sapling descended from a tree planted at the embassy in 1943.
At the US embassy in Bangkok, staff observed a minute of silence. There were similar ceremonies in Manila and Jakarta.
And in London UK Prime Minister Tony Blair and US Secretary of State Colin Powell stood to attention together outside 10 Downing Street as the band of the American School in London played the two national anthems.
Justice
In New York, prayers were offered by Christian, Muslim and Jewish clergy.
"They took down those structures, but they will not take way the spirit," said Rabbi Joseph Potasnik.
About 150 firefighters, police officers and construction workers gathered for the commemoration at Ground Zero.
Amid the cranes and heavy machinery used for excavating the site, bagpipers played "Amazing Grace" as the service concluded.
In Washington, President Bush spoke of America's anger and determination to right "this huge wrong."
"Today the wrong is being righted and justice is being done," he said.
At the Pentagon, a separate ceremony was held three months to the moment after a hijacked plane slammed into the building, killing 189 people.
This happened 34 minutes after the second plane hit the World Trade Center.
A US flag was unfurled in front of a gaping hole in the building, where a huge reconstruction is under way.
US Defence Secretary Donald Rumsfeld addressed the ceremony, saying the victims died "because they were American sons and daughters of the land of liberty."
He went on, " We take strength from their sacrifice."
But after the sombre words, a soldier finished the service with a stirring rendition of "God Bless America."
Pennsylvania, where a fourth airplane crashed after passengers scuffled with the hijackers, was also holding its own memorial.
There was even a tribute in outer space, with American and Russian astronauts pausing to hear a rendition of their national anthems.