D-instantons are used to probe the near-horizon geometry of D3-branes systems on orbifold spaces. For fractional D3-branes, D-instanton calculus correctly reproduces the gauge beta-function and U(I)R anomaly of the corresponding N = 2 non-conformal Super Yang-Mills theories. For D3-branes wrapping the orbifold singularity, D-instantons can be identified with gauge instantons on ALE space, providing evidence of AdS/CFT duality for gauge theories on curved spaces.