In a statement, the palace said it was with "great regret" the Queen would be unable to attend the service.
The statement said: "The Queen, having sprained her back, has decided this morning with great regret that she will not be able to attend today's Remembrance Sunday service at the Cenotaph. Her Majesty is disappointed that she will miss the service.
"As in previous years, a wreath will be laid on Her Majesty's behalf by The Prince of Wales.
"His Royal Highness, along with the Duchess of Cornwall, the Duke and Duchess of Cambridge, the Earl and Countess of Wessex, the Princess Royal and Vice Admiral Sir Tim Laurence, the Duke and Duchess of Gloucester, the Duke of Kent and Princess Alexandra will be present at the Cenotaph today as planned."
It is understood it is a recent sprain and there were concerns over the impact of a car journey and a period of standing on her recovery.
The Queen is said to be deeply disappointed over her absence and she will remain at Windsor Castle.