The Ganondorf fight has two main phases. During the first phase you need to deal 22 or more damage to Ganondorf then have Zelda hit him with a Light Arrow. Ganondorf will then knock Zelda out and the second phase will start. During the second phase you need to deal a certain amount of damage to Ganondorf without the assistance of Zelda. Once this damage has been dealt, Zelda will wake up and you can finish him off.
There are a few ways to go about the first phase. The fastest method uses the Iron Boots although it is the hardest and most risky. Iron Boots are useful as they allow you to land a jump attack in a much shorter period of time.
Thanks to the Iron Boots it is possible to get a two arrow on the first phase, meaning that you only need two arrows from Zelda. This can be seen in the video above and below, although the video above shows a much riskier way of doing it as it is random since it depends upon Ganondorf doing a certain attack at the right time. The video below shows the most consistent way to go about getting a two arrow first phase. The timing on the jump attack and quickspins are semi-precise.