It marked the ninth year "The Simpsons," airing on the Fox network, was named Outstanding Animated Program.
The show won for the episode "The Seemingly Never-Ending Story," which featured flashbacks within flashbacks within flashbacks, the Academy of Television Arts and Sciences said.
The episode beat out the controversial "Trapped in the Closet" episode of "South Park" on Comedy Central. That episode parodied the Church of Scientology and Tom Cruise, one of its most famous adherents.
Soul singer Isaac Hayes, also a Scientologist, quit his role as the voice of the character Chef in protest.
"This is what happens when you don't mock Scientology," "The Simpsons" Executive Producer Al Jean said in accepting his award.
Former "Frasier" star Kelsey Grammer also collected an Emmy for his voice work on "The Simpsons" as Sideshow Bob.