The palace said the monarch, 95, could undertake some light duties during that time, including virtual audiences.
Officials said it is her "firm intention" to attend Remembrance Sunday events on 14 November.
The Queen underwent preliminary medical checks in hospital on 20 October after cancelling a visit to Northern Ireland.
She resumed public engagements on Tuesday this week by meeting ambassadors via video link from Windsor Castle.
But it was announced this week that she will not attend the COP26 climate change summit in Glasgow.
The palace said she would deliver her address to delegates using a recorded video message instead.
In a statement, Buckingham Palace said: "The doctors have advised that Her Majesty can continue to undertake light, desk-based duties during this time, including some virtual audiences, but not to undertake any official visits.
"Her Majesty regrets that this means she will be unable to attend the Festival of Remembrance on Saturday, November 13.
The Queen hosted a Global Investment Summit at Windsor Castle on 19 October.
The next day a spokesman said a planned trip to Northern Ireland had been cancelled, and the monarch had "reluctantly accepted medical advice to rest for the next few days".
Then, in a later statement, Buckingham Palace said she had stayed in hospital on Wednesday night after attending for "some preliminary investigations" and had returned the following day to Windsor Castle, where she was "in good spirits".
Her stay at King Edward VII's Hospital was her first overnight hospital stay in eight years.
The sovereign has maintained a typically busy schedule in October but was recently seen using a walking stick at a Westminster Abbey service, the first time she has done so at a major event.