According to The AP, the speech was meant as a response to threats from radical Muslims who took offence to the pair including a satirical discussion of how to depict the prophet Muhammad in the show's 200th episode.
The response came in some 35 seconds of dialogue between Kyle, Jesus Christ and Santa Claus which was later bleeped out.
"It wasn't some meta-joke on our part," the producers said.
Despite the threat earlier this week, Parker and Stone included Muhammad wearing a bear costume in the episode. Muhammad appeared with his body obscured by a black box, as Muslims consider a physical representation of the prophet to be blasphemous. When the bear costume was removed, it was revealed to be Santa Claus.
"Kyle's customary final speech was about intimidation and fear," the pair said in a statement. "It didn't mention Muhammad at all but it got bleeped. We'll be back next week with a whole new show about something completely different and we'll see what happens to it."
Comedy Central has declined to comment.