The ceremony marked the Queen's return to public service after the coronavirus pandemic forced her to cancel almost all of her engagements.
She knighted Moore with her father's sword and congratulated him on his fundraising efforts, saying, "Thank you very much, an incredible amount you have raised," according to PA Media news agency.
Earlier, the veteran tweeted that he was "ready and looking forward to leaving on what is a very special day."
Moore was accompanied to the ceremony on Friday by daughter Hannah Ingram-Moore, son-in-law Colin Ingram, grandson Benji and granddaughter Georgia, according to PA.
"If I kneel I won't get up again," he said when he left his home for Windsor Castle earlier on Friday.
Moore, who rose to the rank of captain during his military career, was recently promoted to honorary colonel in recognition of his efforts.
Johnson personally recommended to the Queen that Moore be exceptionally honored, according to a Downing Street press release.
"Colonel Tom's fantastic fundraiser broke records, inspired the whole country and provided us all with a bright beacon through the fog of the coronavirus," said Johnson in the statement.
Sarah Dean of CNN and Emma Reynolds contributed to the report.
