© 2020, The Author(s), under exclusive licence to Springer Nature Limited. Ocean circulation critically affects the global climate and atmospheric carbon dioxide through redistribution of heat and carbon in the Earth system. Despite intensive research, the nature of past ocean circulation changes remains elusive. Here we present deep-water carbonate ion concentration reconstructions for widely distributed locations in the Atlantic Ocean, where low carbonate ion concentrations indicate carbon-rich waters. These data show a low-carbonate-ion water mass that extended northward up to about 20° S in the South Atlantic at 3–4 km depth during the Last Glacial Maximum. In combination with radiocarbon ages, neodymium isotopes and carbon isotopes, we conclude that this low-carbonate-ion signal reflects a widespread expansion of carbon-rich Pacific deep waters into the South Atlantic, revealing a glacial deep Atlantic circulation scheme different than commonly considered. Comparison of high-resolution carbonate ion records from different water depths in the South Atlantic indicates that this Pacific deep-water expansion developed from approximately 38,000 to 28,000 years ago. We infer that its associated carbon sequestration may have contributed critically to the contemporaneous decline in atmospheric carbon dioxide, thereby helping to initiate the glacial maximum.