The reading of the names was paused at four points for periods of silence to mark the exact times that the planes hit the towers and when the massive buildings collapsed into piles of rubble and dust.
Similar events took place in Washington, to mark the attack on the Pentagon by a third plane, and Shanksville, Pennsylvania, where a fourth plane crashed after passengers were believed to have fought with hijackers.
"We love you and we miss you," said one woman, mourning the loss of her brother.
"You're still the best, Salvatore," added another, paying tribute to his fallen firefighter brother.
The ceremony was more muted than in past years.
Last year, George Bush visited New York to lay a wreath at the site, but this year attended a private service and observed a moment of silence in Washington.
Meanwhile, US presidential politics and the health of ground zero workers have loomed over the commemorations.
Firefighters and medics who helped in the rescue effort began the recitation of the names after the moment of silence.
Many of those rescuers are now ill with respiratory problems and cancers that they blame on exposure to the fallen towers' toxic dust.
For the first time, the name of a victim who survived the day of the attacks but had died five months later of lung disease was added to the official roll.
Felicia Dunn-Jones, an attorney who was working near the World Trade Center, became the 2,974th person whose death has been linked to the attacks.
Some groups representing the families of victims had opposed giving Rudy Giuliani, a presidential candidate, a speaking role at the commemoration, raising concerns that he would use the platform to promote his presidential aspirations.
He currently leads most of the national polls for the Republican nomination, largely on the strength of his performance on the day of the attacks.
Giuliani has maintained that his appearance was not intended to be political.
He was greeted with a smattering of applause after his brief remarks, which followed the third of the four moments of silence.
"It was a day with no answers, but with an unending line of people who came forward to help one another," said Giuliani, who was in the final weeks of his eight-year tenure at New York mayor at the time of the attacks.