About 200 people gathered Saturday at a Greenwich Village church for the funeral service led by the former Roman Catholic archbishop of New York, Cardinal Edward Egan.
Egan presided over the ceremony at the Church of Saint Joseph as Avonte's parents and brothers sat stoically in a front pew, next to a white casket holding the remains pulled from the East River last week.
"This morning we are grateful to God for Avonte Oquendo, for his life, for his courage, and for the acts of goodness and kindness that his life and his tragic disappearance evoked among us," Egan said. "We know that he is safely in the embrace of the father in heaven and we thank that father in heaven for the years we had with him in our midst."
Many of the volunteers who handed out flyers with his picture on them and helped the search effort arrived at the church Saturday to pay their respects. The city Medical Examiner's Office confirmed Tuesday that DNA tests on the human remains found in Queens matched them to Avonte.
Oquendo's mother was notified early Tuesday afternoon, officials said, and the family's attorney said she was inconsolable. The cause and manner of death are pending.
"She finally just broke down," David Perecman said of his phone call to her. He said it was the first time except for brief moments that he'd seen her cry that much.
Perecman said the family intends to file a wrongful death lawsuit against the city, alleging that school officials failed to monitor the boy or call the police quickly enough when he left the school.
"Now that the inevitable, unfortunately, has occurred, undoubtedly she'll go through a metamorphosis of a sort, and I'm sure she'll get good and angry," he said.
Perecman says he will file the legal claim on behalf of the family. Avonte's remains were found at the edge of the East River last week.
"There were so many things that went wrong, it befuddles the mind," he said.
A teenager shooting photos for a school project noticed the arm on the riverbank last week. Police then found the lower part of a torso and legs on the rocks at low tide, along with black Air Jordan sneakers, white socks and tattered denim jeans. A part of a skull and teeth were recovered a few days later.
For weeks, family, friends and strangers searched for Avonte. His missing poster was plastered in the subways, poles and windshields as part of the all-out effort to find him.
"We all hoped so much that we would find him," said volunteer Waundell Saavedra.
The body parts were found at least 11 miles from where he was last seen. Though the remains were found upriver, past densely-populated shoreline and the Rikers Island jail, the East River is a tidal strait with strong currents that reverse flow many times a day.
The Associated Press contributed to this report.