The issue of output constraints is studied for a flexible-link manipulator in the presence of unknown spatially distributed disturbances. The manipulator can be taken as an Euler-Bernoulli beam and its dynamic is expressed by partial differential equations. On account of the uncertainty of disturbances, we present a disturbance observer to estimate infinite dimensional disturbances on the beam. The observer is proven exponentially stable. Considering the problem of output constraints in the practical engineering, we propose a novel distributed vibration controller based on the disturbance observer to fulfill the position regulation of the joint angle and suppress elastic deflections on the flexible link, while confining the regulating errors of output in a suitable scope that we can assign. The closed-loop system is demonstrated exponentially stable based on an integral-barrier Lyapunov function. Simulations validate the effectiveness of the design scheme.