Well, from all that I've seen and read, I don't think there has ever been any official statement saying what this actually represents. What we can gather is that along with Zant's little head tilt/neck crack, Ganondorf dies.
I don't believe Zant did anything physical to Ganny, it's more of a spiritual, afterlifey thingy (gorgeous description, IK). I believe that when Zant decided to worship Ganny, Zant put his entire faith and him and borrowed his power much like a Religion (sort of). He had a spiritual connection. The head tilt to me was sort of an emotional signal sent from Zant in his afterlife saying "Screw you ******* ur powers suck i don't need this crap I ain't worshipping u no more". So some sort of connection is broken between the two, and Ganny has no more support from Zant. And dies.
Makes sense in my head.