Disney's Finding Nemo has won nine Annie awards, handed out by the International Animated Film Society.
Finding Nemo took more than $800m at the box office
The Pixar-made film, which is also nominated for an Academy Award, won best film, best director and best voice acting for Ellen DeGeneres.
It has become the most successful animated feature of all time, earning more than $800m (£430m) worldwide.
The Simpsons won best animated TV show while Matrix spin-off The Animatrix won an outstanding achievement award.
Finding Nemo tells the story of a clown fish who searches Australia's Great Barrier Reef for his lost son, encountering a hip-talking group of turtles and a trio of remorseful sharks along the way.
Ellen DeGeneres provided the voice of Dory in Finding Nemo
It beat Disney's Brother Bear, Warner Bros.' Looney Tunes: Back in Action, the Japanese anime Millennium Actress and the French film The Triplets of Belleville (Belleville Rendezvous) to the award for film of the year.
The wins come after Pixar and Disney ended their working relationship in acrimonious circumstances.
The two firms had split cost and profit on every Pixar title since Toy Story was released in 1995.
Disney retain the rights to make sequels of some of the films.
But Pixar boss Steve Jobs said: "If you look at the quality of their sequels, like The Lion King, Peter Pan and stuff, it's pretty embarrassing."