This paper proposes an adaptive discrete finite-time synergetic control (ADFTSC) scheme based on a multi-rate sensor fusion estimator for flexible-joint mechanical systems in the presence of unmeasured states and dynamic uncertainties. Multi-rate sensors are employed to observe the system states which cannot be directly obtained by encoders due to the existence of joint flexibilities. By using an extended Kalman filter (EKF), the finite-time synergetic controller is designed based on a sensor fusion estimator which estimates states and parameters of the mechanical system with multi-rate measurements. The proposed controller can guarantee the finite-time convergence of tracking errors by the theoretical derivation. Simulation and experimental studies are included to validate the effectiveness of the proposed approach.