The mechanical design of a robot often influences the choice of control strategy, especially for highdimensional manipulator systems with multiple inputs and outputs. Striking a balance between hardware and software, it remains a significant challenge to design a control framework that is both easy to implement and highperforming. This paper addresses this concern by developing a systematic control architecture for trajectory tracking problems, focusing solely on position measurements. The approach involves constructing a dynamic model of the manipulator in joint space through parameter identification techniques. A non-smooth observer is then devised to estimate unmeasured states, unknown disturbances, and uncertain nonlinear functions in real-time, which are incorporated into a non-smooth feedback control design to provide a control solution. The stability of the system is ensured using the homogeneous system theory and Lyapunov theorems. To validate the effectiveness and feasibility of the proposed tracking control approach, extensive evaluations are conducted on a six-degree-of-freedom (6-DoF) manipulator, including tests for tracking performance and repeatability.