In a previous paper [1] we constructed wave functions of a D-instanton and vertex operators in type IIB matrix model by expanding supersymmetric Wilson line operators. They describe couplings of a Dinstanton and type IIB matrix model to the massless closed string fields, respectively, and form a multiplet of D 10 N 2 supersymmetries. In this paper we consider fermionic backgrounds and condensation of supergravity fields in IIB matrix model by using these wave functions. We start from the type IIB matrix model in a flat background whose matrix size is N 1 N 1, or equivalently the effective action for N 1 D-instantons. We then calculate an effective action for N D-instantons by integrating out 1 Dinstanton (which we call a mean-field D-instanton) with an appropriate wave function and show that various terms can be induced corresponding to the choice of the wave functions. In particular, a ChernSimons-like term is induced when the mean-field D-instanton has a wave function of the antisymmetric tensor field. A fuzzy sphere becomes a classical solution to the equation of motion for the effective action. We also give an interpretation of the above wave functions in the superstring theory side as overlaps of the D-instanton boundary state with the closed string massless states in the Green-Schwarz formalism.