Past studies of the end-Permian extinction (EPE), the largest biotic crisis of the Phanerozoic, have not resolved the timing of events in southern high-latitudes. Here we use palynology coupled with high-precision CA-ID-TIMS dating of euhedral zircons from continental sequences of the Sydney Basin, Australia, to show that the collapse of the austral Permian Glossopteris flora occurred prior to 252.3 Ma (~370 kyrs before the main marine extinction). Weathering proxies indicate that floristic changes occurred during a brief climate perturbation in a regional alluvial landscape that otherwise experienced insubstantial change in fluvial style, insignificant reorganization of the depositional surface, and no abrupt aridification. Palaeoclimate modelling suggests a moderate shift to warmer summer temperatures and amplified seasonality in temperature across the EPE, and warmer and wetter conditions for all seasons into the Early Triassic. The terrestrial EPE and a succeeding peak in Ni concentration in the Sydney Basin correlate, respectively, to the onset of the primary extrusive and intrusive phases of the Siberian Traps Large Igneous Province.