The computer-animated movie, directed by Australian George Miller and featuring the voices of Nicole Kidman, Elijah Wood and Robin Williams, pipped the latest boy wizard adventure, Harry Potter and the Order of the Phoenix.
The penguins were also up against the sewer rat comedy Flushed Away and the fantasy adventure Bridge to Terabithia.
Happy Feet, a box office hit made by Warner Brothers Pictures and Australia's Village Roadshow, won the best animated feature Oscar in February.
Potter also lost out in the video game category. That prize went to Buzz! Junior: Jungle Party, where players compete to build a banana empire and be crowned king of the jungle.
Other winners included: the BBC children's channel CBeebies (TV channel of the year); cartoon character SpongeBob SquarePants (international); and In the Night Garden, the Ragdoll production featuring Igglepiggle.
The winners were announced at a ceremony in London. © 2007 Australian Broadcasting Corporation