Eternal Sonata employs a turn-based combat system. When a character's turn begins, in the lower Party Class Levels the player has a limited amount of time called "tactical time" with which to plan what to do. Once tactical time is over, the action gauge will begin to decrease, giving the player only a few seconds to perform actions, such as moving the character around the battlefield, attacking using normal or special attacks, and using items.
As a character performs normal attacks, a gauge along the right side of the screen will fill with "echoes". The more echoes that fill the gauge, the stronger the next special attack performed will be. When a special attack is performed, the gauge will empty. Later in the game, when the player has gained the ability to perform "Harmony Chains", the player may perform multiple special attacks in succession.
The specific rules of combat are further defined according to the player's current Party Class Level, of which there are six in all. The Party Class Level defines certain aspects such as the amount of tactical time that is available at the beginning of each turn, the amount of time that is available in the action gauge, and the ability to perform Harmony Chains as well as their maximum length. In general, higher Party Levels provide the player with more attack advantages at the cost of less time to perform actions. Enemies are affected in the same way as playable characters by Party Class Levels.
Another aspect of combat is the usage of light and shade. Depending on where a player character is standing, the special attacks of that character will change. For instance, while standing in the sunlight, Polka can use the light special skill Orange Glow to heal an injured ally, but when she is in the shade, her special skill might change to the attack Shade Comet, depending on what skills she has equipped. In addition to shadows cast by geographical features, shade can also be generated by clouds shifting over the battlefield or the shadow of another player character or enemy.
When it is the enemy's turn to attack, if the target of the enemy's attack is not turned away, the player will be given a chance to defend against taking full damage. As the enemy prepares to attack a player character, "Chance" will appear over the character's head, giving the player a split second to press the guard button. If the guard is successful, the character will block a portion of the damage, as well as protect against attack effects such as knock-back. At higher Party Class Levels, the player will on occasion be given the opportunity to perform a counterattack instead of a normal guard. This is signified by the "Chance" icon appearing as a weapon rather than a shield. If successful, the enemy's turn will be interrupted and the player character will go on the attack.
Throughout the game, the player may find items called score pieces hidden in random locations. A score piece is a sampling of sheet music. If the player comes across a non-player character in a town or dungeon that is also in possession of a score piece, the player may choose to play a session with that NPC. The player must then select one of his/her collected score pieces and allow it to play alongside the NPC's score piece. The resultant melody is then graded on a scale ranging from F (lowest) to S (highest). If the player manages to earn a B, A, or S, the NPC will reward the player with an item.
The character Beat has a special ability to snap photographs during battle. Used in the same manner as a typical special attack, the player must aim the camera reticle at an enemy and snap photographs before Beat's action meter depletes. The quality of the photograph is graded depending on how much of the enemy is in the frame, the distance from the enemy, and the angle the shot is taken from. Photographs can then be sold at shops for potentially large sums of money.