Streets near the church, where Mr Kennedy's mother, Jacqueline Kennedy Onassis, used to worship, were jammed with onlookers. The service was private, with no one allowed to witness or record it.
A eulogy to Mr Kennedy was given by his uncle, Edward Kennedy. The Mass was said by the Reverend Charles O'Byrne, who presided over the burial at sea on Thursday of Mr Kennedy, his wife and her sister Lauren Bessette. The mother, father and stepfather of the Bessette sisters were also at the church, with Caroline Kennedy Schlossberg, Mr Kennedy's sister and only surviving child of John F Kennedy.
Bill and Hillary Clinton brought photograph albums as gifts for the families. They included pictures of Mr Kennedy and Carolyn at a White House dinner attended by Tony Blair.
Almost a third of the places in the St Thomas More Church were filled with the extended Kennedy clan.
They included Jean Kennedy Smith, a former ambassador to Ireland, and Kathleen Kennedy Townsend, the Lieutenant-Governor of Maryland.
An onlooker, Heather Sheehan, who had come from Philadelphia to be close to the St Thomas More Church, said: "We're not here to gawk. We're just here to show the Kennedy family our support."