You can't enter the final dungeon until the clock is between 3:45 and 4:00. The dungeon is located in the first cave, the one where you received the Wooden Sword.
When you enter you'll see Ganon grab the Old Man and bust through the northern wall. Head up a screen. If you have six or more Triforce pieces your character will hold the completed Triforce of Courage up and the path will open.
Ganon's behavior is much like in the original The Legend of Zelda. He will slide around the room, invisible, at various angles. At the end of each line of movement he becomes visible, laughs, and takes off on another invisible journey. He follows a clear pattern. If you can intercept him (randomly slashing everywhere will eventually work, too) he'll become blue and visible and be stunned for a bit. Shoot him with a single Silver Arrow and it's all over. Pick up the Triforce of Power 
and continue north. Slash at the flames to free Zelda, then talk to her. Congratulations, you've finished the game!