The retrofitting of selective catalytic reduction (SCR) system to the diesel engine exhaust is becoming necessary in order to reduce the NOx emission. Due to stringent emission norms, the catalyst activity, injection controller, and outlet exhaust gas minimization of SCR system must be significantly improved. In this work, the SCR system for constant-speed stationary diesel engine which is represented as linearized third-order and fourth-order state-space models is controlled using the discrete time super-twisting sliding mode controller (DSTSMC). The engine exhaust NOx emission during the non-road steady cycle (NRSC) drive cycle is applied as input disturbances to the SCR system. Closed loop responses of SCR system obtained for the fourth-order state-space model have higher de-NOx efficiency and lower NH3 slip than the results obtained for the third-order state-space model over 1800s. The injection ratio of ammonia to inlet NOx and the ratio of ammonia reacted to NOx fed by the SCR system are improved for the fourth-order model due to high catalytic activity of fast-SCR.