The monarch said in a birthday card message how the pair have known each other for more than 60 years, having first met in 1958, and their “paths have crossed many times since”.
He was shown writing the card in a clip at the conservationist’s birthday concert at the Royal Albert Hall in London.
The 77-year-old royal said Sir David has revealed “the beauty and wonders of nature to audiences around the world in new and marvellous ways”.
He added that the broadcaster has shared the King’s “determination to highlight the urgent need to protect and preserve” Earth for future generations.
Read more: See pictures from Sir David’s life
The King said he and the Queen were “delighted” to learn he will be celebrating the milestone and on behalf of the whole country wished him a very happy birthday.
Animals could then be seen delivering the letter across land, sea and air, before Sir David could be seen holding his royal birthday card aloft in the venue.
The card’s journey was initially thwarted by a fallen tree – only to be saved by the creatures, including an eagle, a fox, a red squirrel and an otter that travel across the UK to ensure that the wildlife presenter receives his royal dispatch.
The King and Queen also shared a carousel of photographs of Sir David on the official Royal Family Instagram account.
The caption read: “Wishing Sir David Attenborough a very happy 100th birthday. Enjoy your special celebration this evening!”
In a birthday tribute, stars including Morgan Freeman, Dame Judi Dench and Spice Girl Geri Halliwell-Horner, joined in the celebration and teamed up with conservation charity WWF.
A one-minute-long video featured a spoken word reinterpretation of Louis Armstrong’s What a Wonderful World.
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Sir David Beckham also marked Sir David’s big day with a post on his Instagram account captioned: “Happy 100th Birthday to our National Treasure.”
Meanwhile, fellow environmentalist and Hollywood star Leonardo DiCaprio called Sir David “one of the most enduring champions of our shared planet” in an Instagram post.
The Royal Albert Hall celebration was just one of many events to mark the broadcaster’s birthday, including a takeover of the Piccadilly Lights in central London, displaying a birthday message for Sir David.
Sir David said he has been “completely overwhelmed” by goodwill messages and thanked well wishers “most sincerely”.
