Ocean acidification (OA) reduces the concentration of seawater carbonate ions that stony corals need to produce their calcium carbonate skeletons, and is considered a significant threat to the functional integrity of coral reef ecosystems. However, detection and attribution of OA impact on corals in nature are confounded by concurrent environmental changes, including ocean warming. Here we use a numerical model to isolate the effects of OA and temperature, and show that OA alone has caused 13±3% decline in the skeletal density of massive Porites corals on the Great Barrier Reef since 1950. This OA-induced thinning of coral skeletons, also evident in Porites from the South China Sea but not in the central equatorial Pacific, reflects enhanced acidification of reef water relative to the surrounding open ocean. Our finding reinforces concerns that even corals that might survive multiple heatwaves are structurally weakened and increasingly vulnerable to the compounding effects of climate change.