The game utilizes complete use of the Nintendo DS stylus to control the characters' movements and actions, especially during lightsaber combat; there are also special action sequences in which the player must complete quick-time events by quickly making the correct stylus strokes on-screen to help the characters avoid a dangerous situation. Lightsaber attacks are executed with rapid taps of the stylus, with three unique attack positions (low, middle and high), and players must perform even faster taps to overpower enemies with melee weapons and make them vulnerable to attacks. Each character has special lightsaber combo moves that can occur if the player inputs a particular sequence of 4 attacks at differing positions, such as middle-middle-high-high. Certain hands-on activities that the characters must perform, such as cutting a hole through a door or hacking control panels, are experienced as minigames that are mainly played with dragging motions of the stylus, as opposed to tapping.
Jedi Alliance features nine levels in which the player must select two of the following six Jedi characters —Anakin Skywalker, Ahsoka Tano, Obi-Wan Kenobi, Mace Windu, Plo Koon, and Kit Fisto—to proceed through a story original to the game. There are two types of Jedi, combat and environmental, and the player is encouraged to use different combinations of Jedi type pairs (combat-combat, combat-environmental or environmental-environmental) to uncover new areas and collectibles throughout the game. Collecting Force orbs will charge up a powerful Force attack to inflict massive damage on an enemy; the amount of orbs needed to charge it and the damage it inflicts for a particular Jedi pair will increase every time the player completes a level with it. During some moments, R2-D2 and C-3PO are also playable, though their abilities are limited. As the player completes levels, as well as each of their 9 side objectives (such as getting through the level without dying or finding all of a particular collectible), they can unlock new costumes for the characters, concept art for the game and special cheats.