At first I didn't know what it meant, but now I think I'm starting to understand it a little more.
I think it symbolized Ganondorf's fall and Zant breaking away from his clutches.Ganondorf and Zant are connected by their power. When Zant was destroyed by Midna, he claimed as long as Ganon was alive, he could come back. They shared their power, though Ganon controlled him(pretty much.)
When Ganondorf was stabbed, it showed Zant cracking his neck. I think this is also a symbolism that Zant's power, as well as Ganondorf's is gone and that Ganondorf's life itself is gone.
I actually liked how they did this. Ganondorf gets stabbed first of all, and then you get this sort of illusion showing Zant crack his neck. It's very creepy...