Specialists worked for four months to individually clean each frame of the 1968 film by hand, The Beatles' holding company Apple Corps Ltd. told The AP.
The specialists reportedly chose not to use automated software because of the delicate nature of the hand-drawn artwork, the company added.
John Lasseter, Pixar chief, said: "As a fan of animation and as a filmmaker, I tip my hat to the artists of Yellow Submarine, whose revolutionary work helped pave the way for the fantastically diverse world of animation that we all enjoy today."
The fantasy movie, which features cartoon versions of The Beatles and images from some of their songs, is currently out of print.
The film features some of the band's greatest hits including 'Lucy in the Sky With Diamonds', 'Eleanor Rigby' and 'When I'm Sixty-Four'.
The DVD will be released on May 28, and the film's soundtrack album will be re-issued on CD on the same day.
Watch The Beatles' 'Yellow Submarine' video below: