Significant nanoscale disorder of Cu and Ca atomic substitution is observed in CaCu(3)Ti(4)O(12), based on our integrated study using quantitative electron diffraction and extended x-ray absorption fine structure. Unambiguous identification of this previously omitted disorder is made possible by the unique sensitivity of these probes to valence-electron distribution and short-range order. Furthermore, first-principles-based theoretical analysis indicates that the Ca-site Cu atoms possess partially filled degenerate e(g) states, suggesting significant boost of dielectric response from additional low-energy electronic contributions. Our study points to a new route of enhancing dielectric response in transitional metal oxides by exploiting the strong electronic correlation beyond classical static pictures.