She was greeted by the Dean of Westminster, the Very Reverend Dr John Hall, at the the front of the central London abbey before the procession on Tuesday.
Camilla was greeted by Westminster Sub Dean, the Venerable David Stanton.
The service, attended by more than 2,000 people, celebrated 750 years since Edward the Confessor's original church was rebuilt under the reign of King Henry III.
The Gothic abbey was consecrated on October 13, 1269.
Abigail Wallace, Captain of the Queen's Scholars at Westminster School, presented a bouquet of roses to the Queen at the start of the service.
She then placed it on the shrine of St Edward the Confessor on behalf of the Queen.
The Very Reverend Dr Hall said it was "wonderful" to have the Queen and duchess attend the service.
"The Queen is the visitor of Westminster Abbey and she has a wonderful and close association with the abbey," he told the PA news agency after the service.
He said the Queen has been "very gracious and generous" by attending three to four services a year in the abbey.
"(The Queen is) always smiling and warm, engaging in the most extraordinary way really," he said.
"It's very special."
In his sermon the Very Rev Dr Hall said Tuesday's service celebrated the church and it's long history within the life of London, the nation and its worldwide influence.
"The abbey stands with the Palace of Westminster, Whitehall and the Supreme Court at the heart of our nation," he said.
He also urged the UK Government to increase funding for Muslim schools.
"Too many Muslim children are being educated in poorly funded independent schools," he said. "There should be a clear duty on Government to encourage excellent state-funded Muslim schools."
Treasures including a fragment of the shroud from the shrine of St Edward the Confessor, an Anglo-Saxon royal charter document and a medieval manuscript were laid on the High Altar during the 45-minute ceremony.
After the service, the Queen received yellow posies from Margaret Payne, 10. The duchess was given flowers by Margaret's nine-year-old brother Theo.
Among the state dignitaries in attendance were Black Rod Sarah Clarke; Lord Fowler, the Lord Speaker; Lord Lieutenant of Greater London Sir Kenneth Olisa and Lord Mayor of Westminster Ruth Bush.
Catholic Archbishop of Westminster Cardinal Vincent Nichols and Coptic Archbishop Anba Angaelos were also in attendance.
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