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Due to several merits, the pneumatic actuation systems are commonly used to drive the positioning stages. However, one of the critical demerits of the pneumatic systems is the problem of the compressibility, which results in the flow disturbance. Another problem of the positioning stage can be addressed to the vibration which occurs due to the active condition of the base plate. Therefore, this paper concerns the mentioned two issues in a pneumatic positioning stage. In order to suppress the flow disturbance and reduce the horizontal vibration of the stage due to the reaction force, a combined control scheme is proposed. This scheme is composed of the fusion of flow disturbance observer (FDOB) and base plate jerk feedback (BPJFB) schemes. An enhanced methodology is provided to efficiently implement the combined scheme. The experimental results show the effectiveness of the proposed method.