If you reference the diagram of Penny's endoskeleton, she has a rib cage of sorts and cranium that seem to be much more robust than the rest, so I would guess that her most vital systems are in there. After the match with Pyrrha, it seemed that everything from the rib cage up on her torso and head was okay. My hypothesis is that her main power supplies may have been lower down in her torso and got disconnected, so she had to shut down.
I saw this picture a couple of days before the episode aired and when I saw how Penny got torn apart in the same way as this pic I was like... Whooooa.... WIZAAAAARD!