In this paper, we propose a method to apply the Input Shaping Technique (IST) to multi-input multi-output (MIMO) systems. In MIMO systems, there is a high possibility of multi-mode residual vibration. The IST filter designed for this multi mode may need a longer time to suppress the residual vibration. Previous works prove that we can shorten the time lag by using negative sequence. This negative sequence, however, causes another problem - it requires excessive control input. In this paper, we provide a remedy to reduce the size of control input by limiting the reference input by limiting the reference input and its derivative. The result of simulations and experiments on a 2 link flexible arm confirmed the effectiveness of the proposed method.