The formation of the Antarctic Circumpolar Current (ACC) is critical for the evolution of the global climate, but the timing of its onset is not well constrained. Here, we present new seismic evidence of widespread Late Eocene to Oligocene marine diagenetic chert in sedimentary drift deposits east of New Zealand indicating prolonged periods of blooms of siliceous microorganisms starting ~36 million years ago (Ma). These major blooms reflect the initiation of the arrival and upwelling of northern-sourced, nutrient-rich deep equatorial Pacific waters at the high latitudes of the South Pacific. We show that this change in circulation was linked to the initiation of a proto-ACC, which occurred ~6 Ma earlier than the currently estimated onset of the ACC at 30 Ma. We propose that the associated increased primary productivity and carbon burial facilitated atmospheric carbon dioxide reduction contributing to the expansion of Antarctic Ice Sheet at the Eocene-Oligocene Transition.