At ground zero 200 children and young adults, each of whom had lost a relative in the attacks, read out the names of 2,792 people who died two years ago. At the Pentagon the defence secretary, Donald Rumsfeld, presided over a ceremony, while church bells rang out across Shanksville in rural Pennsylvania, the site closest to the crash of hijacked flight UA93.
In Washington DC, President George Bush attended an early-morning church service followed by the observance of a moment's silence.
Afterwards Mr Bush and his wife, Laura, emerged from the White House alongside the vice-president, Dick Cheney, and his wife, Lynne, to join hundreds of members of his staff on the grass of the south lawn.
The president bowed his head at 8:46am, the time the first terrorist-hijacked plane struck the World Trade Centre, then the four turned without speaking and returned inside. Later, the president travelled a few miles to an army medical centre for a private session with soldiers treated for wounds suffered in Iraq.
The subdued tone was in stark contrast with last year, when Mr Bush visited all three sites - ground zero in New York, the Pentagon and Pennsylvania.
Aides say the new approach was in keeping with the president's view that the day should be solely about the families.
But it also reflected what President Warren Harding referred to more than 80 years ago as a "return to normalcy". America has been deeply affected by the terrorist attacks in a number of ways. But with the distance of time the nation is largely returning to its old routines, even if in a slightly more cautious way.
Americans woke up to a state department warning of possible al-Qaida attacks against US interests. And yet, unlike the first anniversary, when many passengers refused to fly, airlines said yesterday that passenger volumes were much like any other midweek day. Polls show Americans still live in fear of another terrorist attack but issues relating to the economy, unemployment and health insurance have once again taken precedence.
Elsewhere in the country, cities, towns and rural communities paid tribute in similar fashion. Twisted steel recovered from the ruins was shipped to other states for memorials from North Dakota to Florida, including a New Mexico church that uses two trade centre beams as part of its bell tower.
In Toledo, Ohio, the mayor's wife began reading the names of the victims in a ceremony which took hours and was followed by the release of white doves.
At Boston's Logan international airport, where two of the hijacked planes took off, there was a moment's silence.
"Think not of the empty chair but the people who filled those chairs," said Jim Ognowski, whose pilot brother, John, was killed when the plane he was flying hit the World Trade Centre. "We must find the inner strength and courage to live our own lives in a way which they would have wanted."
But the focus was on New York, where the commemoration began with a vigil at St Paul's Chapel, which once stood in the shadow of the twin towers. Families began arriving at the site well before yesterday's ceremony, many wearing ribbons of white or black, symbolising mourning, or yellow for hope.
They carried flowers - daisies, petunias and roses to leave during the ceremony.
At sunrise yesterday around 200 people sat quietly at an ecumenical service in a small park not far from ground zero which included a violinist, readings of poems, and songs by a children's choir. "I was hoping to get a couple of minutes to face up to all the emotions of the day and to continue the process of trying to adjust," said Nathaniel Hupert.
The ceremonies were due to end at the following sunrise, with two shafts of light beamed skywards from the ground zero at sunset.
In between came the litany of names read by children and relatives of the victims, who would end their contributions with their loved ones' names, often adding: "I love you and I miss you."
Lynn Morris lost her husband, Seth, in the attack. She looked up articles so that her two children, Madilynn, 11, and Kyle, 9, could match faces to names as they read them out. "It's amazing the strength they have developed over the years," she said.