I've always interpreted it as him severing the tie between the two of them. You know, the tie that connected their lives. Ganondorf basically poured his life force into Zant, which is what allowed Zant to be resurrected without cease. Of course, Midna obliterated Zant with the Fused Shadows to where he couldn't be physically revived, but that life connection he and Ganondorf shared wasn't severed, so his spirit was still connected. When Ganondorf was mortally wounded and unable to do anything, all that was left from him dying was that life connection. So Zant, realizing he'd been played for a fool the whole time, ended the connection, thereby delivering the final blow of sorts to Ganondorf.
I didn't come to this conclusion upon playing the game for the first time -- it actually confused the hell out of me -- but after my second playthrough, this was the conclusion I came to and my thoughts on the subject have never changed. And they probably never will be. Only Nintendo directly saying something otherwise will change my thoughts on this, as the game heavily implies this is what went down. It's not exactly official, but I don't see much of an alternative.