Silver's deal with Warner Bros will be over by the end of 2012, which also means that his own production company Silver Pictures will no longer be housed on the studio's Burbank lot.
Their long partnership reached breaking point when Silver started complaining about the way Warner Bros was handling the marketing and distribution of Sherlock Holmes: A Game of Shadows, for which he served as producer, reports Deadline.
He also allegedly disapproved of how the first teaser for The Dark Knight Rises, a Warner Bros movie, was paired with the IMAX release of Paramount's Mission: Impossible - Ghost Protocol.
Both Sherlock Holmes 2 and M:I4 were released on the same month of last year.
"That commitment to M:I4 was made through IMAX eight months earlier," one studio executive said. "And then Paramount moved up the date.
"What Joel did was to paint a picture of Sherlock 2 as a failure, calling up agencies bitching, stirring up the town against Warner Bros by claiming marketing had not eventized the movie."
During his 25 years at Warner Bros, Silver produced a wide array of films including big franchises like The Matrix, Die Hard and Lethal Weapon, as well as The Losers, Speed Racer and V for Vendetta.
Watch the trailer for Sherlock Holmes: A Game of Shadows below: