This paper presents a robust adaptive output feedback tracking controller for the flexible-joint robot manipulators to deal with the unknown upper bounds of parameter uncertainties and external disturbances. With applying the singular perturbation theory and integral manifold concept, the complex nonlinear coupled system of the flexible-joint robot manipulators is divided into a slow subsystem and a fast subsystem. A robust adaptive control scheme based on an improved linear parameterization expression is designed for the slow subsystem, and a saturation function is applied in the robust control term to make the torque output smooth. In the meantime, different from the previous approaches, the second-order derivative term of elastic torque is avoided by using the proposed computed torque method, which simplifies the implementation of the fast control law. Moreover, to carry out the whole control system with only position measurements, an approximate differential filter is involved to generate pseudo velocity signals for links and joint motors. In addition, an explicit but strict stability proof of the control system based on the theory of singularly perturbed systems is presented. Finally, simulation results verify the superior dynamic performance of the proposed controller.