I am unsure here because as we've seen Ganondorf has been sealed in other dimensions reduced to almost nothing and literally stabbed and had his neck broken and everytime he's returned. One of the more likely ways is what happened in Wind Waker, he ended up turning to stone instead of actually dying. So maybe if the master sword is embedded fully in his body that would end the cycle as fully but short of that. Maybe separation of his mortal remains (HW is not canon so no, no mention of that sub-par plot). I think the best bet would be to pull a Lorule and destroy the Triforce completely not split into pieces but complete destruction, seeing as Ganon/Ganondorf seems to rely overly much on the ToP to sustain him if that was destroyed then he'd be nothing greater than a Gerudo sorcerer (given his mothers Twinrova in OOT)