It is well-known that the instanton-induced superpotential is generated in the massless limit of supersymmetric QCD, thus violating the non-renormalization theorem. This superpotential has been calculated previously by an indirect method: taking its form as uniquely determined by U(1) symmetries then obtaining numerical coefficient from the calculation of the quasi-Goldstone fermion mass. The latter arises already from a single instanton. However, the effective scalar potential is an instanton-anti-instanton effect. In the present paper we show that the vacuum of the theory is a dilute gas of instanton-anti-instanton molecules. The effective scalar potential is calculated directly as an instanton-anti-instanton effect. The scalar vev is fixed from this potential by the minimization procedure. This vev is shown to satisfy the Konishi anomaly identity in accordance with the Witten index analysis.