Arc-continent collision in Southeast Asia during the Neogene may have driven global cooling through chemical weathering of freshly exposed ophiolites resulting in atmospheric CO2 removal. Yet, little is known about the cause-and-effect relationships between erosion and the long-term evolution of tectonics and climate in this region. Here, we present an 8-million-year record of seawater chemistry and sediment provenance from the eastern Indian Ocean, near the outflow of Indonesian Throughflow waters. Using geochemical analyses of foraminiferal shells and grain size–specific detrital fractions, we show that erosion and chemical weathering of ophiolitic rocks markedly increased after 4 million years (Ma), coincident with widespread island emergence and gradual strengthening of Pacific zonal sea-surface temperature gradients. Together with supportive evidence for enhanced mafic weathering at that time from re-analysis of the seawater 87Sr/86Sr curve, this finding suggests that island uplift and hydroclimate change in the western Pacific contributed to maintaining high atmospheric CO2 consumption throughout the late Neogene.