In this paper, a novel backstepping terminal super-twisting sliding mode (TSTSM) with high order sliding mode observer (HOSMO) is proposed to control the two degrees of freedom (DOFs) Serial Elastic Actuator (SEA), inspired by a lower limb of humanoid robots. First, the dynamic model, extended from our previous study, is presented for developing the control algorithm. Secondly, the backstepping technique is utilized to separate the overall system into two subsystems. One of the challenges of SEA is to deal with the evident oscillations caused by the elastic element, which might lead to the degrading performance of load position control. In order to reduce this adverse effect, a TSTSM is proposed to control the position tracking of two subsystems. The advantages of TSTSM are the finite-time convergence despite the bounded perturbation and the dramatic reduction of the chattering phenomenon. To construct and implement the TSTSM controller, it requires the knowledge of all states, which is not available in the current lower limb system setup. Therefore, a HOSMO is utilized to estimate the unknown states. Finally, experiment results are carried out to assess the effectiveness of the proposed controller and compare it with those of different control schemes.