In this paper, we present a novel approach to fault-tolerant terminal sliding mode tracking control for flexible joint manipulators (FJM), incorporating finite-time detection and estimation of perturbations. Unlike previous approaches, our method estimates the fault and disturbance separately within a specific finite time, along with finite-time convergence of the flexible joints to the desired values. This paper extends previous works by providing a more applicable solution to finite-time control of FJMs. The proposed approach involves the design of an observer-based terminal sliding mode control strategy. The key contributions of this work include achieving four finite-time convergence together: finite-time disturbance estimation, finite-time fault estimation, finite-time convergence of the observer and finite-time tracking in manipulator. To do this, the system is divided into two subsystems, and a new composite observer is first introduced for finite-time estimation of the fault and disturbance components separately. Following this, a novel robust-adaptive sliding mode controller is developed, incorporating a third-order sliding mode surface, a continuous control strategy, and visually estimated fault signals. The formulated observer-based control law ensures the convergence of the posture variables of the flexible joint robotic manipulator, encompassing its angles, to the desired values within a finite time frame. The control strategy integrates an adaptive law to rectify estimation errors. The efficacy of the proposed method demonstrated through its application to the FJM system, with simulation results highlighting its effectiveness.