The 100-year-old, who raised almost £33m for NHS charities, was taken to Bedford Hospital after requiring help with his breathing on Sunday.
The Queen led tributes to Capt Sir Tom, “recognising the inspiration he provided for the whole nation and others across the world”.
His daughters said they “shared laughter and tears” with their father in their final few hours together.
Capt Sir Tom tested positive for Covid-19 last week. His family said due to other medication he was receiving for pneumonia, he was unable to be vaccinated.
The Army veteran won the nation’s hearts by walking 100 laps of his garden in Marston Moretaine last year during the first lockdown, raising money for NHS Charities Together.
A Buckingham Palace spokeswoman said: “Her Majesty very much enjoyed meeting Capt Sir Tom and his family at Windsor last year. Her thoughts, and those of the royal family, are with them, recognising the inspiration he provided for the whole nation and others across the world.”
In a statement, Prime Minister Boris Johnson said: “Captain Sir Tom Moore was a hero in the truest sense of the word. In the dark days of the Second World War he fought for freedom and in the face of this country’s deepest post-war crisis he united us all, he cheered us all up, and he embodied the triumph of the human spirit.
“He became not just a national inspiration but a beacon of hope for the world. Our thoughts are with his daughter Hannah and all his family.”
The flag above 10 Downing Street has been flying at half-mast following the news.
Boris Johnson has spoken to Capt Sir Tom’s daughter Mrs Ingram-Moore to offer his condolences.
Archbishop of Canterbury Justin Welby pays tribute to Captain Sir Tom, describing him as “the very best of us”.
He says: “I am deeply saddened to hear that Sir Captain Tom Moore has died.
“I pray for his family and friends, and I join millions across the country in mourning with them.
“Captain Tom was the very best of us. His courage, compassion, resilience, hope and generosity have been an inspiration to millions – and an example to us all.
“Where he walked a nation followed.
“I give thanks to God for such a long life, so well lived. May Captain Tom rest in peace.”
