Actuator modules of humanoid robots have relatively higher joint elasticity than those of industrial robots. Such joint elasticity could lead to negative effects on both the tracking performance and stability for walking. Especially, unstable contact between the foot and the ground caused by joint elasticity is a critical problem to decrease the stability of position-controlled humanoid robots. In this sense, this paper introduces a novel control scheme for position-controlled humanoid robots by which we can obtain not only enhance compliance capability for unknown contact but also suppress vibration caused by the joint elasticity. To estimate the disturbance caused by external forces and modeling errors between the actual system and the nominal system, a disturbance observer based estimator is designed at each joint. Furthermore, a linear feedback controller with the flexible joint model and a gravity compensator is considered to minimize vibration and deflection due to the joint elasticity. The proposed control scheme was implemented on our humanoid robot, DYROS-JET, and its performance was demonstrated by improved performance for both stability and vibration suppression during dynamic walking and stepping on objects.