The Queen has passed by human rights protesters on her way to a lunch with Commonwealth heads of state.
She attended the event alone as the Duke of Edinburgh remained in hospital with a bladder infection.
She was joined by more than 70 guests, including Prime Minister David Cameron and leaders from across the association of nations, as they arrived to angry scenes.
Hundreds of Tamil and human rights campaigners gathered outside Marlborough House in central London in opposition to Sri Lankan President Mahinda Rajapakse's presence at the meal.
Mr Rajapakse was jeered as he swept through the main gate in a Range Rover. His car did not carry a flag because of security concerns.
The Queen seemed relaxed as she was handed a bouquet of flowers by nine-year-old Aduke Badale, the daughter of a member of the Commonwealth Secretariat staff.
The Queen spent a brief moment with Mr Rajapakse and appeared to fleetingly shake hands with him as she met guests at a reception in the Blenheim Saloon inside Marlborough House.
Heads of state and representatives from Australia, Canada and the African nations were welcomed by Commonwealth Secretary-General Kamalesh Sharma.
After a performance of the Commonwealth song, Stronger as One, by soprano Laura Wright, the Queen was presented with a bronze plaque to mark the jubilee.
The presentation was followed by a "family photo" which was arranged informally and not dictated by protocol. The Sri Lankan president stood alongside Mr Cameron for the photo opportunity.