Biological processes in Southern Ocean surface waters have widespread impacts on global productivity and oceanic CO2 storage. Here, we demonstrate that biological calcification in the Southern Ocean exerts a strong control the global distribution of alkalinity. The signature of Southern Ocean calcification is evident in observations as a depletion of potential alkalinity within portions of Subantarctic Mode and Intermediate water. Experiments with an ocean general circulation model indicate that calcification and subsequent sinking of biogenic carbonate in this region effectively transfers alkalinity between the upper and lower cells of the meridional overturning circulation. Southern Ocean calcification traps alkalinity in the deep ocean; decreasing calcification permits more alkalinity to leak out from the Southern Ocean, yielding increased alkalinity in the upper cell and low-latitude surface waters. These processes have implications for the atmosphere-ocean partitioning of carbon. Reductions in Southern Ocean calcification increase the buffer capacity of surface waters globally, thereby enhancing the ocean’s ability to absorb carbon from the atmosphere. This study highlights the critical role of Southern Ocean calcification in determining global alkalinity distributions, demonstrating that changes in this process have the potential for widespread consequences impacting air-sea partitioning of CO2.