i dont think he died and here i my reasons. the "weak"point was because of the sages which could act as a type of seal.so when link stabed ganondorf i think his soul literally went into the sword and so the ToP lest cause thee was no one in that body which would yes give death to ganondorf so...
ok i no you say theres two ganons but if there was one like a lot of ppl say than how does ganondorf come back after tp btw this is for the ppl who believe in the 1 ganon thing