This paper investigates the problem of finite-time trajectory tracking for fully actuated autonomous surface vehicles without the velocity measurements, in the presence of uncertain parameters and complex environmental disturbances. Firstly, a generalized nonlinear finite-time extended state observer is proposed to recover the velocities and synthetic disturbances simultaneously. The generalized structure can further enhance the estimation accuracy and the observation errors are proved to be finite-time uniformly ultimately bounded stable. Then, a two-loop control law is developed by using virtual velocity command and fast non-singular integral terminal sliding controller. The observer is integrated with the controller to overcome the problem of unavailable surge, sway, yaw velocities and to rapidly reject disturbances, thereby contributing to fast and accurate trajectory tracking of the vehicle. Theoretical analysis for finite-time stability of the closed-loop system is rigorously derived through the Lyapunov’s stability theory. Finally, comparative simulation results are given to illustrate the effectiveness and superiority of the proposed control approach.