Prince Philip has been interred in the royal vault at St George's Chapel alongside the remains of 24 other royals including three kings.
But it will likely not be his permanent resting place.
Prince Philip's coffin was placed on a catafalque on a marble slab and lowered into the vault by an electric motor on Saturday.
Horns were played as his coffin was lowered down.
A blessing was given by the Archbishop of Canterbury before the choir sang the national anthem God Save the Queen.
The members of the royal family looked up as the choir sang while the Queen bowed her head.
The 94-year-old monarch was then led out of the church by the archbishop and followed by her family members.
Prince William, her grandson, was seen glancing back at the vault as he left his pew.
The vault was created between 1804 and 1810 for George III, who died in 1820 and is one of three kings buried there.
The other two are George IV and William IV.
The vault has also been the temporary resting place for almost 30 royals, including Philip's mother, Princess Andrew of Greece.
Her remains were transferred to the convent on the Mount of Olives in Jerusalem, where they now lie near her aunt, Grand Duchess Serge of Russia.
King George VI, the father of Queen Elizabeth II, was interred in the royal vault for 17 years before his remains were moved to the King George VI Memorial Chapel at St George's in 1969.
His wife, Queen Elizabeth, the Queen Mother and daughter Princess Margaret were interred alongside him after they died in 2002.
After the death of Queen Elizabeth II, she and Philip are expected to be buried in the Royal Burial Ground on the Frogmore Estate close to Windsor Castle.
Philip died on April 9 at age 99.
Australian Associated Press