It was reported she wanted to do the skit to show the public how much their celebrations of her reign meant to her. Filmmakers praised her for her "wit, warmth and generosity" in going along with the idea.
Paddington Bear tweeted his tribute at today's news of the monarch's death: "Thank you Ma'am, for everything."
The sketch showed Paddington, spraying cream from a chocolate Èclair over a palace footman, and as he shows Her Majesty what he hides beneath his hat - his famous marmalade sandwiches - the Queen goes one better saying: "So do I" and, opening her handbag, tells him: "I keep mine in here."
The short film was a moving fan favourite. Paddington congratulated the Queen on her reign: "Happy Jubilee Ma'am. And thank you for everything."
The monarch replied: "That's very kind."
The sequence ended with the Queen and Paddington using a spoon to tap out the beat of Queen's We Will Rock You on a china teacup.
The Queen spent half a day filming the top-secret sketch, and palace aides declined to explain how she managed to converse with Paddington.
It was reminiscent of the James Bond sketch in 2012, when she played herself opposite Daniel Craig to seemingly "parachute" into the Olympic Games.
The film began with Bond arriving at Buckingham Palace in an iconic black cab and walking down a hallway flanked by the royal's beloved Corgi dogs.
He is greeted by Queen Elizabeth, wearing a pale peach dress, with the words "Good evening Mr Bond."
The pair then walk outside to a waiting helicopter, past a number of iconic London sights including Tower Bridge, Westminster Abbey and the London Eye before arriving at the Olympic Stadium.
It then appears as if Queen Elizabeth jumps out of the plane followed by Bond as the theme tune from the spy franchise plays.
However, the royal revealed the joke when she and her husband Prince Philip appeared to loud cheers, where they walked down the steps in the stadium to their seats before the English national anthem was played.
