The queen appeared on the balcony of Buckingham Palace with Prince Charles, his wife Camilla, Prince William, his wife Kate, and Prince Harry. The queen was without Prince Philip, who was hospitalized on Monday with a bladder infection.
A noisy Lancaster bomber, four Spitfire fighters and a Hurricane fighter - all recalling the nation's battle for survival in World War II - flew over the palace. They were followed by nine jets spewing red, white and blue smoke.
Thousands of well wishers lined the streets of London to see the royal family arrive at St Paul's Cathedral for the service of thanksgiving. The Archbishop of Canterbury, Rowan Williams, praised the queen for bringing happiness to the nation.
"We are marking six decades of living proof that public service is possible and that it is a place where happiness can be found," Williams said.
In a rare televised statement, the queen said the celebrations had been "a humbling experience."
"I will continue to treasure and draw inspiration from the countless kindnesses shown to me in this country and throughout the Commonwealth," the monarch said in the two-minute broadcast, shown in Britain and the 54-nation Commonwealth of its former colonies.
President Barack Obama also paid tribute to the queen, saying, "While many presidents and prime ministers have come and gone, your majesty's reign has endured."
The Associated Press contributed to this report.