We compiled carbon isotope records from the North Atlantic, South Atlantic, and Pacific oceans to estimate changes in vertical and interbasinal δ13C gradients for the last 9 Myr. Benthic δ13C values of deep water in the South Atlantic decreased in a series of steps at ~7, 2.75, and 1.55 Ma away from the North Atlantic and toward the Pacific. The benthic δ13C of intermediate water in the South Atlantic evolved differently from deep waters, resulting in an increase in the intermediate-to-deep δ13C gradient (Δ13CID). The Δ13CID increased in steps at ~2.75 and 1.55 Ma, marking the development and intensification of a chemical divide in the Atlantic Ocean between well-ventilated intermediate water and poorly ventilated deep water. We suggest these changes in interbasinal and vertical gradients resulted from decreasing Northern Component Water and reduced ventilation of Southern Component Water (SCW). The latter was caused by several interrelated processes in Antarctic sources areas, including increased sea ice cover, enhanced surface water stratification, decreased Ekman-induced upwelling, and reduced vertical mixing across the thermocline. Because Antarctic surface water processes and deepwater ventilation rates ultimately influence atmospheric CO2 concentration, these processes may have acted as a positive feedback that contributed to the major cooling steps in late Neogene climate.