The final battle with Yuga takes place after he has fused with Ganon, making him far more powerful than before. The battle is split into two phases.
In his first phase, Yuga will swipe at Link with his trident and occasionally throw it at him to deal damage. Link simply needs to attack him with any of his damage-dealing items to end this phase. After taking several blows, Yuga will usually teleport away and reappear somewhere else in the arena. When badly damaged, Yuga will also teleport away and drop several orbs of dark energy on Link, who must move around the arena to avoid the damaging explosions they make upon contact with the ground. After several orbs have fallen, Yuga will return to the battle and continue his other attack patterns.
The second phase of the battle begins when the apparently defeated Yuga betrays Princess Hilda and absorbs her Triforce of Wisdom. More powerful than ever, Yuga now attacks by launching large energy balls at Link, who must counter by playing Dead Man's Volley with the projectiles. When Yuga fails to deflect his attack, he will retreat into the wall, at which point Princess Zelda's portrait gifts him with the Bow of Light. Link must then merge into the wall, face Yuga, and fire a Light Arrow. While Yuga struggles with the arrow, Link must quickly merge out of the wall and back in behind Yuga, where he can fire another arrow into the villain's back. Yuga will be knocked out of the wall, and Link can damage him normally for a few moments.
After Yuga recovers, Link must repeat the process of Dead Man's Volley to force Yuga into the wall. This time, Yuga will respond to Link's Light Arrow by charging at him - at this point, Link must merge out of the wall as Yuga passes by, allowing him to merge back in and fire a Light Arrow at Yuga's back. After being forced out of the wall, Yuga is again vulnerable to Link's attacks for a moment.
The third round of Dead Man's Volley with Yuga is made more difficult by the addition of a second energy ball - Link must deflect both attacks into Yuga to force him back into the wall. When Link merges with the wall, Yuga will counter any Light Arrows aimed at his front, while also turning around the moment Link approaches from behind. In order to hit Yuga, Link must fire a Light Arrow away from the villain; due to the circular room they are battling in, the arrow will fly all the way around the wall and damage Yuga. After knocking Yuga out of the wall, Link only has to hit him once more with his sword to end the battle.
Interestingly, the final battles against Yuga are in the opposite order of the final battles in The Legend of Zelda: A Link to the Past. In the first phase, Yuga uses a move set similar to that of Ganon in A Link to the Past, and in the second phase, he uses a move set similar to Agahnim's.