The end-Permian mass extinction horizon is marked by an abrupt shift in style of carbonate sedimentation and a negative excursion in the carbon isotope (δ13C) composition of carbonate minerals. Several extinction scenarios consistent with these observations have been put forward. Secular variation in the calcium isotope (δ44/40Ca) composition of marine sediments provides a tool for distinguishing among these possibilities and thereby constraining the causes of mass extinction. Here we report δ44/40Ca across the Permian-Triassic boundary from marine limestone in south China. The δ44/40Ca exhibits a transient negative excursion of ∼0.3‰ over a few hundred thousand years or less, which we interpret to reflect a change in the global δ44/40Ca composition of seawater. CO2-driven ocean acidification best explains the coincidence of the δ44/40Ca excursion with negative excursions in the δ13C of carbonates and organic matter and the preferential extinction of heavily calcified marine animals. Calcium isotope constraints on carbon cycle calculations suggest that the average δ13C of CO2 released was heavier than -28‰ and more likely near -15‰; these values indicate a source containing substantial amounts of mantle- or carbonate-derived carbon. Collectively, the results point toward Siberian Trap volcanism as the trigger of mass extinction.