Recent small angle neutron scattering suggests that the spin structure in the A phase of MnSi is a so-called triple-Q state, i.e., a superposition of three helices under 120 degrees. Model calculations indicate that this structure in fact is a lattice of so-called Skyrmions, i.e., a lattice of topologically stable knots in the spin structure. We report a distinct additional contribution to the Hall effect in the temperature and magnetic field range of the proposed Skyrmion lattice, where such a contribution is neither seen nor expected for a normal helical state. Our Hall effect measurements constitute a direct observation of a topologically quantized Berry phase that identifies the spin structure seen in neutron scattering as the proposed Skyrmion lattice.