This paper presents a perturbation estimator in sliding mode control system and applies it to vibration control of a flexible arm subjected to torque disturbance. The proposed estimator is featured by an integrated average value of the imposed perturbation over a certain sampling period. By implementing this type of estimator, undesirable chattering phenomenon can be effectively alleviated in the estimation process. In addition, the proposed method offers a flexibility for tuning the ratio of the estimation sampling time to the control input sampling time. In order to demonstrate the effectiveness of the proposed methodology, a single-link flexible arm is constructed. After formulating the governing equation of motion, a sliding mode controller which is integrated with the proposed estimator is designed. Vibration control performances of the flexible arm subjected to sinusoidal torque disturbances are evaluated through both computer simulation and experimental realization.