She is understood to have been advised by doctors not to attend Royal Variety because of the late start and long running time.
A source said that the Queen is “naturally disappointed to miss the evening’s entertainments, and sends her sincere apologies to all those involved, but is a great believer that ‘the show must go on’.
“She hopes to be back to full strength and regular public duties very soon.”
The King will now attend the event alone, while the Queen will remain in London on Friday and will then travel to Sandringham for the following week as planned.
This year, the Royal Variety Performance will be hosted by Amanda Holden and Alan Carr at the Royal Albert Hall, with performances including Sir Elton John and Sophie Ellis-Bextor.
Members of the Royal family attend the event each year, in a tradition dating back to George V and Queen Mary.
Last year, the performance was watched by the Prince and Princess of Wales, with the Crown Princess and Prince of Sweden as their guests.
The Queen fell ill after a 10-day tour to Australia and Samoa, and a short stay at an Indian health retreat on the way home.
She was diagnosed with a chest infection and pulled out of several events including the National Service of Remembrance at the Cenotaph and the movie premiere of Gladiator II.
This week, she made a short appearance at a reception for the Booker Prize foundation where she said she was “on the mend”.
“I’m getting much better,” she said on Monday. “Bit of sort of coughing going on but I really wanted to be here.”
She appeared well at a Buckingham Palace reception for young essay writers on Thursday, and is said to be on the “road to recovery” but still “a little under the weather”.