A closed-loop identification procedure for multivariable systems utilizing set-point change in a rectangular pulse type, is proposed and applied to two example systems, The identified model composed of transfer functions of the first order plus dead time model is decoupled and separated into multiple single-input/single-output (SISO) loops. Then, the SISO PI/PID control loops are tuned using combined open-loop and closed-loop tuning guidelines. The performance of the control system is examined in the set-point tracking and regulatory performances and compared with the BLT tuning method. It is found that the performance of this study is better than that of the BLT tuning. Also, it is proved that the proposed identification method requires short identification time and leaves no disturbance in process output.