This paper investigates the control issue of the trajectory tracking of vertical take-off and landing (VTOL) unmanned aerial vehicles (UAVs) in the presence of partial propeller fault and external disturbance. In particular, a robust passive fault-tolerant control strategy is proposed by introducing a first-order filter based dynamics estimator. First, a bounded force command is exploited by employing a new smooth saturation function in the output of the estimator. A sufficient condition in terms of a specified parameter selection criteria is provided to ensure the non-singularity extraction of the command attitude. Then, a torque command is applied to the attitude loop tracking. Since there is merely one filter parameter involved in the dynamics estimator, the practical implementation and parameter tuning can be significantly simplified. Stability analysis indicates that the proposed control strategy guarantees the semi-globally ultimately bounded tracking of VTOL UAVs subject to partial propeller fault and external disturbance. Simulation and experiment results with comparison examples are performed to validate the effectiveness of the proposed strategy. Experimental results show that the proposed strategy achieves the trajectory tracking with a good performance (mean deviation 0.0074 m and standard deviation 0.1202 m) in the presence of 35 % propeller fault and 4 m/s persistent wind disturbance.