This paper mainly focuses on designing an active vibration control for a flexible-link manipulator in the presence of input constraint and unknown spatially infinite dimensional disturbances. The manipulator we studied can be taken as an Euler-Bernoulli beam, the dynamic model of which has the form of partial differential equations. As the existence of spatially infinite dimensional disturbances on the beam, we first design a disturbance observer to estimate infinite dimensional disturbances. The proposed disturbance observer is guaranteed exponentially stable. Then, taking input saturation into account, a novel disturbance-observer-based controller is developed to regulate the joint angular position and rapidly suppress vibrations on the beam, which is the main contribution of this study. The closed-loop system is validated asymptotically stable by theoretical analysis. The effectiveness of the proposed scheme is demonstrated by numerical simulations.