Yes, and the true mystery lies in how they got to Comedy Central. I mean, it says that the FOX people saw their small cartoon. But it looks somewhat.. simplistic to me. Weren't there many others who did similar cartoons?
Although it was early 90s, Flash wasn't around much.
Southpark was originally construction paper cutouts -- I think Trey animated using stop-motion techniques. They use some 3D software now. I KNOW the cartoon is 99% 2D and the animation could be done in Flash, but they use something more robust.
The reason I used Flash as an example is that a lot of cartoons on the net are made with it. So South Park ties in with them thematically, in a way, since Trey and Matt started it out the same way, with one of their cartoons, Jesus vs. Santa, serving as a Christmas ecard.
And yes, it's done in Maya. It was done in PowerAnimator before Maya.