Rich Moore also was named best director for the animated comedy about a video game villain who dreams of being a hero, and Alan Tudyk won the Annie for voice acting as King Candy in the box-office hit. Phil Johnston and Jennifer Lee won for their screenplay and Henry Jackman, Skrillex, Adam Young, Matthew Thiessen, Jamie Houston and Yasushi Akimoto won for music.
"Wreck-It Ralph" also won the Producers Guild of America Award last week and is nominated for an Academy Award for animated feature.
Disney's "Paperman," which is also an Oscar nominee, won for best animated short.
Other feature film winners included Andy Hayes, Carl Hooper and David Lipton for animated effects in animated production for "Rise of the Guardians," and Jerome Platteaux, John Sigurdson, Ryan Hopkins, Raul Essig and Mark Chataway for animated effects in a live action production for "The Avengers."
On the TV side, "Despicable Me: Minion Mayhem" won the Annie for best animated special production, while "Dragons: Riders of Berk: How to Pick Your Dragon' '' took home the honor for best animated television production for children.
"Robot Chicken 'DC Comics Special' " was the recipient of the best general audience animated television production award, and John Eng won for best directing in an animated television/broadcast production for "Dragons: Riders of Berk: Animal House." Trey Parker received the Annie for writing in an animated television/broadcast production for "South Park: Jewpacabra."
Kristen Schall earned the Annie for voice acting in an animated television/broadcast production as Mabel Pines in "Gravity Falls: Tourist Trapped."
Film historian/critic Leonard Maltin and voice actors Rob Paulsey and Maurice Lemarche hosted the ceremony, which is presented by the ASIFA-Hollywood.