An output feedback control (OFC) is presented for a linear stochastic system with known disturbance and applied to a flexible spacecraft for the reduction of residual vibration while allowing the natural deflection during operation. By converting the tracking problem into regulator problem, the OFC minimizes the expected value of a guadratic objective function composing of error stats which always remain on the intersection of sliding hypersurfaces. For the numerical evaluation with a flexible spacecraft, a large slewing maneuver strategy is devised with a tracking model for nominal trajectory and start-cost-stop strategy for economical maneuver in conjunction with the input shaping technique. The performance and efficacy of the proposed control scheme are illustrated with the comparison of different maneuver strategies.