The Paleocene-Eocene thermal maximum (PETM) has been attributed to the rapid release of ~2000 × 109 metric tons of carbon in the form of methane. In theory, oxidation and ocean absorption of this carbon should have lowered deep-sea pH, thereby triggering a rapid (<10,000-year) shoaling of the calcite compensation depth (CCD), followed by gradual recovery. Here we present geochemical data from five new South Atlantic deep-sea sections that constrain the timing and extent of massive sea-floor carbonate dissolution coincident with the PETM. The sections, from between 2.7 and 4.8 kilometers water depth, are marked by a prominent clay layer, the character of which indicates that the CCD shoaled rapidly (<10,000 years) by more than 2 kilometers and recovered gradually (>100,000 years). These findings indicate that a large mass of carbon (>>2000 × 109 metric tons of carbon) dissolved in the ocean at the Paleocene-Eocene boundary and that permanent sequestration of this carbon occurred through silicate weathering feedback.