Radiocarbon in the atmosphere is regulated largely by ocean circulation, which controls the sequestration of carbon dioxide (CO2) in the deep sea through atmosphere–ocean carbon exchange. During the last glaciation, lower atmospheric CO2 levels were accompanied by increased atmospheric radiocarbon concentrations that have been attributed to greater storage of CO2 in a poorly ventilated abyssal ocean1, 2. The end of the ice age was marked by a rapid increase in atmospheric CO2 concentrations2 that coincided with reduced 14C/12C ratios (Δ14C) in the atmosphere3, suggesting the release of very ‘old’ (14C-depleted) CO2 from the deep ocean to the atmosphere3. Here we present radiocarbon records of surface and intermediate-depth waters from two sediment cores in the southwest Pacific and Southern oceans. We find a steady 170 per mil decrease in Δ14C that precedes and roughly equals in magnitude the decrease in the atmospheric radiocarbon signal during the early stages of the glacial–interglacial climatic transition. The atmospheric decrease in the radiocarbon signal coincides with regionally intensified upwelling and marine biological productivity4, suggesting that CO2 released by means of deep water upwelling in the Southern Ocean lost most of its original depleted-14C imprint as a result of exchange and isotopic equilibration with the atmosphere. Our data imply that the deglacial 14C depletion previously identified in the eastern tropical North Pacific5 must have involved contributions from sources other than the previously suggested carbon release by way of a deep Southern Ocean pathway5, and may reflect the expanded influence of the 14C-depleted North Pacific carbon reservoir across this interval. Accordingly, shallow water masses advecting north across the South Pacific in the early deglaciation had little or no residual 14C-depleted signals owing to degassing of CO2 and biological uptake in the Southern Ocean.