Buckingham Palace said the 95-year-old monarch made the decision not to attend the Remembrance Sunday service at the Cenotaph “with great regret” and was said to be deeply disappointed to miss it.
It is understood the Queen has not received hospital treatment for her back and the injury is unrelated to recent medical advice for her to rest.
She was ordered to rest by royal doctors just over three weeks ago and spent a night in hospital on October 20 undergoing preliminary tests.
The Queen was due to watch the service at the war memorial in central London from the balcony of the Foreign, Commonwealth and Development Office building.
It is the first time in 22 years that the head of state has missed the Remembrance Sunday ceremony.
She would have been on public view for about 20 minutes if the format followed previous years.
It is thought that a back sprain would have made it difficult for the Queen to have endured a car journey to London followed by a period of standing.
Prime Minister Boris Johnson told a Downing Street press conference later on Sunday that the Queen was “very well”.
He said: “I know that everybody will be wanting to offer their best wishes to Her Majesty the Queen and I just wanted to reassure everybody by saying that I did see the Queen for an audience last week on Wednesday in Windsor and she’s very well.
“It shouldn’t need saying but I just wanted to say it anyway.”
While the Prince of Wales, the Duchess of Cornwall, the Duke and Duchess of Cambridge and other royals gathered for the Cenotaph service, the monarch watched the proceedings on television from Windsor Castle.
The Queen has missed several other key events, including the Festival of Remembrance at the Royal Albert Hall on Saturday evening.
The palace announced during the week that the Queen will also miss the General Synod.
It is believed to be the first time the Queen has missed her five-yearly visit to the General Synod in its 51-year history.
She was well enough to travel by helicopter to Sandringham on November 4 for a long-planned weekend away, where she was seen, in her trademark off-duty headscarf, being driven around the estate.
On October 20, she pulled out of a trip to Northern Ireland and then missed the Cop26 climate summit in Glasgow at the start of November.
The Queen has been carrying out light duties including dealing with her red boxes of papers and conducting a handful of virtual audiences.
It is understood she hopes to continue as planned with her schedule of light official duties next week.
On Thursday, the palace said the Queen would attend Sunday’s service, and had previously said it was her “firm intention” to be there.
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 started the Second World War as a schoolgirl but ended it in uniform as a junior commander with the Auxiliary Territorial Service.
On Sunday morning, less than two hours before the service in Whitehall, the palace 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.”
The Queen recorded a powerful speech for Cop26, calling on world leaders to “rise above” politics and achieve “true statesmanship” by tackling climate change.
In her video message, she paid tribute to her “dear late husband”, the Duke of Edinburgh, for his environmental awareness in raising the issue more than 50 years ago.
Philip died aged 99 seven months ago, leaving the Queen mourning her life-long companion.
The Queen no longer lays a wreath at the Cenotaph herself.
In 2017, the Prince of Wales began placing one on his mother’s behalf as she watched from the balcony of the Foreign and Commonwealth Office building instead.
The change was seen as a subtle shift of head-of-state duties.
The Queen has only missed six other Cenotaph ceremonies during her reign, on four occasions when she was on overseas visits: to Ghana in 1961, Brazil in 1968, Kenya in 1983 and South Africa in 1999.
She was not present during the 1959 and 1963 services as she was pregnant with her two youngest children.
Baroness Scotland, the Commonwealth secretary-general, said there would be “sadness” that the Queen has had to pull out of attending the service.
Asked on Sky News’ Trevor Phillips On Sunday programme if it would be “disappointing” for many veterans not to have the monarch in attendance, Baroness Scotland said: “Absolutely.
“The Queen is adored, rightly. She has shown total commitment to the Commonwealth and she is much loved.
“So, an opportunity like this, to see her and to pay homage for what she herself also did, because people do forget that she was an engineer, she was making her contribution as well.
“I think there will be a lot of sadness but everyone will be wishing her well, everyone will want to see her again. She is the beating heart of most of the love that is in the Commonwealth, so we do wish her well.”