Wouldn't the wound itself be just as fatal as the inflicting of it? Once the ToP leaves, he has a gaping hole in his chest and several internal organs punctured.One thing that makes me believe Ganondorf does not die at the end of TP is that the ToP leaves his hand after he has been stabbed with the Master Sword; we don't necessarily know the exact reason for its departure from his hand -- its departure may be tied to his defeat rather than death. If the fatality of the blow is determined by when the blow is dealt, he was "protected" under the ToP because he still had it at the time of being stabbed. We know that TWW Ganondorf died without the ToP in his hand -- it had left to form the full Triforce. Then the Master Sword was embedded in his skull, which has happened before in OoT, although Ganondorf had the ToP at the time. Perhaps it is the fact that the Master Sword remains embedded in Ganondorf that constitutes his confirmed death, because the weapon that is designed to defeat him is constantly inflicting a wound. However, unlike in TWW, the Master Sword is removed from Ganondorf's body (it can be seen returned to Link's sheath at 4:43 of this video: http://www.youtube.com/watch?v=EmxxIZapJXc ); if the wound to his stomach was not fatal, it is possible that he could have survived unbeknownst to Link and Zelda.
And precedent shows that the critical period for the ToP's power is just after being stabbed. When he was executed, he was first stabbed, and then the ToP lit up and he was revived. At the end, he was stabbed, and the ToP disappeared, implying the opposite.