Compressors, pumps etc often generate noise and vibration due to periodic disturbances. It is known that vibration suppressing systems such as repetitive control are effective in suppressing periodic disturbances. However, there is no report about methods that can make control performance deterioration as small as possible when the control inputs of the vibration suppression system are saturated. This paper develops a disturbance observer that is effectively suppressing periodic disturbances, and proposes a method that can make control performance deterioration minimal even if the control inputs are saturated. First, the proposed system estimates disturbances using the disturbance observer. Next the estimated disturbances are passed into a filter of unity gain and zero phase change at the disturbance's frequencies, and are added into the control input in order to cancel the periodic disturbance. Some motor system simulations show that the phase of the estimated disturbances corresponds to that of the periodic disturbances so that the method can make control performance deterioration minimal. The method is appropriate to rotational machine systems such as compressors and pumps in which vibration and noise should be avoided.