Yes and no. It is 3d but 2d, kinda. Each character moves on a 2D plane relative to the enemy they have targeted, but the enemies aren't on a line (and neither are the allies), so you will move in 3D relative to other enemies, and party members.
So it has 3d movement in combat, but you can only move in the 3rd dimension as a side effect of your 2d movement.