When you get into the chamber, Ganon appears for only a moment, and then becomes invisible, shooting fireballs at you from various locations in the room. You need to have the magic sword equipped and run around the room, slashing at the air until you hit him. When you hit him, he will appear for a second (to show you that you hit him) and he will be a greenish color. Continue to hack and slash at the air until he appears, but this time is BROWN. When he appears BROWN, equip your silver arrows (you should have gotten the arrows in the 9th dungeon, and you MUST have them to defeat Ganon). You only need to hit him once with these arrows to beat him for good.