For its greenhouse effects, atmospheric CO2 can critically influence the global climate on millennial and centennial timescales. Pleistocene atmospheric CO2 variations must involve changes in ocean storage of carbon, but the mechanisms and pathways of carbon transfer between the oceanic and atmospheric reservoirs are poorly understood due, in part, to complications associated with interpretation of carbonate system proxy data. Here we employ a recently developed approach to reconstruct upper Atlantic air–sea CO2 exchange signatures through the last deglaciation. Using this approach, proxy and model data each suggest that there was a net release of CO2 via the Atlantic sector of the Southern Ocean during the early deglaciation, which probably contributed to the millennial-scale atmospheric CO2 rise during Heinrich Stadial 1 at ~18.0–14.7 kyr ago. Moreover, our data reveal a previously unrecognized mechanism for the centennial-scale atmospheric CO2 rise at the onset of the Bølling warming event around 14.7 kyr ago, namely, the expansion of Antarctic Intermediate Water, a water mass that is especially inefficient at sequestering atmospheric CO2. Our findings highlight the role of the Southern Ocean outgassing and intermediate water-mass production and volume variations in governing millennial- and centennial-timescale atmospheric CO2 rises during the last deglaciation.