We study D-instanton contributions to supergraviton scattering amplitudes in the ten-dimensional type IIB superstring theory beyond the leading non-perturbative order. In particular, we determine the one-D-instanton contribution to maximal R-symmetry violating (MRV) amplitudes with arbitrary momenta at the first subleading order in string coupling, as well as the effects of a D-/anti-D-instanton pair at leading nontrivial order in the momentum expansion. These results confirm a number of predictions of S-duality, and unveil some previously unknown pieces of type IIB string amplitudes.Our computation is based on the Neveu-Schwarz-Ramond formalism with picture changing operators and vertical integration. The naive on-shell prescription for Dinstanton mediated amplitudes, based on integration over the moduli space of worldsheet geometries as well as the moduli space of D-instanton boundary conditions, suffers from potential open string divergences and regularization ambiguities that are in principle resolved in the framework of open+closed superstring field theory. In this paper, the "on-shell ambiguities" of one-D-instanton MRV amplitudes are resolved by arguments involving supersymmetry and soft limits, part of which is verified by a string field theoretic computation in a highly nontrivial manner.