Senior members of the Royal Family said their final farewells in a private service at St George's Chapel on Tuesday.
It followed a day of national mourning during which more than a million people turned out to pay their respects along the funeral route and many more observed two minutes' silence in the Queen Mother's honour.
The Archbishop of Canterbury paid tribute to her gifts of "strength, dignity and laughter" at the funeral service in Westminster Abbey in London.
Dr George Carey told the congregation, and the many thousands listening to broadcasts across the world, that the Queen Mother was like the sun "bathing us in her warm glow".
"We come here to mourn but also to give thanks, to celebrate the person and her life - both filled with such a rich sense of fun and joy and the music of laughter," he said.
Tone of thanksgiving
The Prince of Wales appeared to be on the brink of tears while the Queen listened intently with her head bowed.
A poem by an unknown author helped set the tone of thanksgiving for the Queen Mother's 101 remarkable years.
It read: "You can shed tears that she is gone or you can smile because she has lived.
"You can close your eyes and pray that she'll come back or you can open your eyes and see all she's left."
The Queen Mother's coffin was taken from Westminster Hall to Westminster Abbey accompanied by pipers, and borne on the same gun carriage used for her husband George VI's funeral 50 years ago.
Supermarkets closed
Nine senior members of the Royal Family walked behind the coffin in a military procession of impressive pageantry.
Prince William, 19, and 17-year-old Prince Harry were in the funeral cortege.
Queen Mother's return to Windsor
The Duke of Edinburgh led the royal mourners who also included the Duke of York, the Earl of Wessex, Viscount Linley, 40, and Peter Phillips, the Princess Royal's 24-year-old son.
They passed thousands of ordinary people, many of whom had queued overnight to pay their last respects.
Around the UK, millions observed two minutes' silence at 1130 BST - the moment the Queen Mother's coffin arrived at the abbey.
Supermarkets closed their doors, buses and trains were halted, and many offices and schools fell silent.
Westminster Abbey's Tenor Bell tolled for every year of the Queen Mother's life.
The Queen Mother's coffin then began the sad 23-mile journey to Windsor, accompanied by Prince Charles.
Daughter's ashes
Hundreds of thousands of people lined the route, many throwing flowers as the black hearse carrying her coffin passed by.
The Queen Mother was buried alongside her husband in St George's chapel.
The ashes of her daughter Princess Margaret, who died in February, were interred at the same time in the Royal Vault.
Afterwards Prince Charles left en route for one of his grandmother's residences at Birkhall on the Balmoral estate, where he has chosen to spend some time alone in reflection.
He is expected to spend a week there and to be joined by Camilla Parker Bowles.
Other members of the family were expected to resume royal duties on Wednesday.
The small George VI side chapel at Windsor where the Queen Mother was buried will be open from 1000 BST on Wednesday.
Members of the public will be able to pay their final respects before the official period of mourning ends on 19 April.