It was part of an interfaith memorial service on Sunday marking the end of the recovery effort.
The ceremony included the lighting of four candles: one for peace and three to honor rescue workers, the families and the more than 2,800 people who died after the attacks of Sept. 11.
After the ceremony, some family members threw flowers over the fence into the seven-story pit that is all that remains of the twin towers. Others attached bouquets to the fence. One woman clutched it and sobbed, screaming out a name as she looked at the site.
Tom Resta, who lost his brother John in the attacks, said the memorial and the others that have been held are all bittersweet.
``I feel they're necessary, but each one is a knife in the heart,'' he said. ``These things are just too painful.''
Dennis McKeon, director of the St. Clare's Church WTC Outreach program, which organized Sunday's ceremony, said the event was especially important to families whose loved ones have not been identified.
``Starting next week, this is going to be a construction site, so this is their last chance to say goodbye,'' McKeon said.
About 1,100 victims have been identified and nearly 20,000 body parts were recovered during the excavation of the 16-acre site, which ends after more than eight months of round-the-clock work.
Jennifer Nilsen, 33, lost her husband Troy Nilsen, a Cantor Fitzgerald worker whose remains have not been identified.
``It's real important, you know, saying goodbye to my husband, which I never wanted to do,'' she said. ``I'm glad this was done today.''
On Thursday, thousands of people attended a service organized by the city to mark the end of the cleanup at the site and to honor the rescue workers.
An empty, flag-draped stretcher symbolizing the victims whose remains have not been recovered was carried out of the pit, followed by the trade center's last steel beam, draped in black cloth and a flag. Nilsen said she was grateful for the interfaith memorial, because caring for her two children made it impossible to attend the Thursday ceremony. Several victims' groups had criticized Mayor Michael Bloomberg for not holding the city service on a weekend, when they said it would be easier for families to attend.
The mayor said he chose a weekday because he did not want the service to interfere with religious observances. Before Sunday's service, he said he wouldn't attend because he didn't ``want to politicize anything.''
Among the dignitaries at the family memorial were former Mayor Rudolph Giuliani and Sen. Charles Schumer.
The search for human remains will continue at the Staten Island landfill where 1.8 million tons of debris were taken by trucks and barges, city officials said. The cleanup finished more than three months earlier than expected and, at less than $750 million, at a fraction of the estimated cost.