Conventional fuzzy controllers for motion tracking utilize generally two input variables (position error and velocity error) to deal with highly nonlinear and time-varying dynamics associated with complex mechanical motion with multi-DOF. This results in some tracking errors at steady state, in general, mainly due to friction existing in mechanical systems. To eliminate the steady-state tracking errors, a variable structure fuzzy control algorithm is proposed using three input variables (position error, velocity error, and integral of position errors) and a switching logic between two inputs and three inputs. Simulation and experimental studies have been conducted to show the validity of the proposed control logic using a direct-drive SCARA manipulator with two degree-of-freedom. It has been shown that the proposed fuzzy control logic has significantly improved motion-tracking performance of the mechanical system when it is applied to complex polygon-tracking in Cartesian space with inverse kinematics and path planning.