Hints:
Ganon stomps around the battlefield, swinging his swords at anything in his path. It takes Ganon little over a second from the moment he winds up to the time he strikes; use a single Rolling Attack or Backflip to get Link out of range. If Ganon hits Link, this is bad news for you Life Meter. If he hits the rubble, the smashed pieces will reveal either Magic Jars, Bombs, Arrows or Fairies. This can be effective if you're low on power.
There are two ways to defeat Ganon: the Light Arrow Method or the Run-In Method. The Light Arrow Method is the easiest way to defeat Ganon, but the Run-In method doesn't place your Magic Meter or Quiver under any strain. In either event, the choice is entirely upto you.
LIGHT ARROW METHOD
Firstly, make sure that you're lined up face-to-face with Ganon. Now, fire a Light Arrow into his eyes; Ganon will now be stunned for several seconds, more than enough time for you to reach his sole weak point. Charge in and with the Hammer or Biggoron's Sword, strike Ganon's rainbow-coloured tail.
After enough hits, Ganon will collapse and the wall of flame around the battlefield will falter. You can now run to Zelda and recover the Master Sword. Beware, though, as the wall of flame will rise as soon as you re-enter the battle! The only way to avoid this is by using a Rolling Attack at the right moment, but it's just as easy to cut your loses by wearing the Goron Tunic as you head back.
From now on, keep firing Light Arrows into Ganon's eyes, but make the strikes on his tail with the Master Sword. After enough hits, Ganon will collapse and Zelda will hold him down with her power. Now use the Master Sword to deliver the final blow.
RUN-IN METHOD
The Run-In is difficult at first, but is useful as it allows you to defeat Ganon without burning your Magic Meter. If you'd like to practice the Run-In against Ganon, there is a way to have an endless battle against Ganon: fight to the point where you recover the Master Sword. Now use the Run-In Method, but use Biggoron's Sword or the Hammer; though everything looks like Ganon has sustained damage, he's still as healthy as before!
The Run-In is difficult to master, and consists of the following steps: