As compensation for the lack of online, Spike has added a new 'Disc Fusion' system to the PlayStation 2 version. Players can fight against anyone from around the globe with a ranking system showing the player's current standing compared to anyone else who has played online. The Wii version features online multiplayer capability, the first game in the series to have such a feature. You can also change the aura of your character. There are also several other time differences, such as dawn and afternoon. Night and day stages allow for more accurate battles in Dragon History, as well as the ability to transform into a Great Ape by using the moon.

Battle Replay allows players to capture their favorite fights and save them to an SD card to view later on. Several new notable features include Battle Replay, night and day stages, the Wii's online capability, and Disc Fusion.

Gamestop offered an exclusive version with a bonus DVD containing the top 10 television series battles as voted by fans on the release date. Ryo Mito stated that the game would feature never-before-seen characters made exclusively for the game, referring to the Saiyans' Great Ape forms. Budokai Tenkaichi 3 features 161 characters, almost the largest in any fighting game being topped by Fire Pro Wrestling Returns and Tobal 2, for which Akira Toriyama was a designer.

Dragon center gaming mode