The problem of trajectory tracking for a class of nonlinear systems in the presence of un-modeled dynamics, parameter variations and even the actuator faults is investigated in this paper. A novel fault-tolerant control scheme is proposed by combining the nominal model-based controller and time-delay controller, which are adopted to achieve the real-time dynamic compensation and guarantee the robust stability of the controlled systems, respectively. Moreover, high-quality differential signals are unavailable in the presence of disturbances and measurement noise, which limit the performance of closed-loop systems in practice. Therefore, an extended state observer (ESO) is introduced to obtain high-quality differential signal estimations based on position measurements only. Furthermore, the effectiveness of the proposed novel control scheme is verified by testing in the spacecraft attitude tracking system.