Spider-Man
The film was helmed by Bob Persichetti, Peter Ramsey and Rodney Rothman and is only the third time since the category was introduced in 2007 that wasn't awarded to a film from Disney or Pixar.
The other nominations this year included Incredibles 2, Ralph Breaks the Internet, Isle of Dogs and Mirai, The Hollywood Reporter wrote.
The film centres on the African-American/Puerto Rican Brooklyn teen Miles Morales as Spider-Man and has been well received for its fresh story and visual style.
Earlier winners of the award since its introduction include How to Train Your Dragon 2 and The Adventures of TinTin.
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