The Southern Ocean plays a crucial role in regulating atmospheric CO2 on centennial to millennial time scales. However, observations of sufficient resolution to explore this have been lacking. Here, we report high-resolution, multiproxy records based on precisely dated deep-sea corals from the Southern Ocean. Paired deep (∆14C and 11B) and surface (15N) proxy data point to enhanced upwelling coupled with reduced efficiency of the biological pump at 14.6 and 11.7 thousand years (ka) ago, which would have facilitated rapid carbon release to the atmosphere. Transient periods of unusually well-ventilated waters in the deep Southern Ocean occurred at 16.3 and 12.8 ka ago. Contemporaneous atmospheric carbon records indicate that these Southern Ocean ventilation events are also important in releasing respired carbon from the deep ocean to the atmosphere. Our results thus highlight two distinct modes of Southern Ocean circulation and biogeochemistry associated with centennial-scale atmospheric CO2 jumps during the last deglaciation.