She had been due to attend the Commonwealth Day Observance at the Abbey where High Commissioners from across the globe watched a keynote address from Sir Richard Branson, but instead left it to the Duke of Edinburgh to represent the Royal Family.
She later made her first official public appearance for more than a week, describing the charter as capturing “the core values and aspirations” of the family of nations, before putting her name to it.
The Queen looked well and in good spirits when she arrived at Marlborough House in central London, home of the Commonwealth, with Prince Philip, for the signing.
Before the ceremony began she told guests from across the globe: “The Charter I will sign today, on behalf of you all, represents a significant milestone as the Commonwealth continues its journey of development and renewal.
“We have now, for the first time, a single document that captures the core values and aspirations of the Commonwealth and all its members.”
The monarch spent 24 hours in hospital last week being treated for the stomach bug, which leaves sufferers with vomiting and diarrhoea.
Buckingham Palace had said on Friday that the Queen would attend the service and it was “business as usual”.
The 86-year-old was struck down by the stomach bug just over a week ago and spent last Sunday night at the private King Edward VII’s Hospital in central London before being discharged on Monday.
Concerns were raised about the Queen’s general wellbeing as it was the first time she had been admitted to hospital in almost 10 years.
But she left the hospital looking well and cheerful.
Her engagements for last week were cancelled, including a brief visit to Rome to meet Italy’s president.
A Buckingham Palace spokeswoman said: “This time last week she was in hospital, but she’s in great spirits and apart from this is in good health and will be going to the reception in the evening.
“It’s just the tail end of the symptoms, her condition has not worsened at all.”
The Palace added: “The Queen hopes to undertake some of her official engagements planned for the rest of this week.”