The 95-year-old monarch was ordered to rest by royal doctors just over three weeks ago, and spent a night in hospital on October 20 undergoing preliminary tests.
She returned to Windsor Castle on Tuesday after a long-planned weekend away at her Sandringham estate in Norfolk.
Buckingham Palace said: “The Queen will attend the annual Remembrance Day Service at the Cenotaph on Sunday 14th November.
“As in previous years Her Majesty will view the service from the balcony of the Foreign, Commonwealth and Development Office building.
“Mindful of her doctors’ recent advice, the Queen has decided not to attend the General Synod Service and Opening Session on Tuesday 16th November.
“The Earl of Wessex will attend as planned.”
The Palace said previously it was the Queen’s “firm intention” to attend the annual wreath-laying service in Whitehall, which falls on November 14 this year, and honours Britain’s war dead.
The monarch, who lived through the Second World War as a teenager, is head of the Armed Forces and attaches great importance to the poignant service and to commemorating the sacrifices made by fallen servicemen and women.
She was already confirmed to be missing the annual Festival of Remembrance at the Royal Albert Hall on Saturday evening. Instead, The Prince of Wales and the Duchess of Cornwall will lead other members of the royal family including the Duke and Duchess of Cambridge, the Earl and Countess of Wessex and the Princess Royal at the event.
She conducted a Privy Council meeting by video link from Windsor on Wednesday afternoon, with ministers including Lord President of the Council Jacob Rees-Mogg and Education Secretary Nadhim Zahawi among others.
Earlier on Thursday, Prince Charles reassured a bystander about the Queen’s condition as he met members of the public in Brixton.
Charles was greeted by crowds of people as he left a branch of NatWest bank in south London after an engagement for the Prince’s Trust on Thursday.
One man asked him: “Prince Charles How is your mother?”
The heir to the throne gave him an encouraging pat on the arm, and appeared to say: “She’s alright, thank you.”