Unravelling causes for absolute plate velocity change and continental dynamic topography change is challenging because of the interdependence of large-scale geodynamic driving processes. Here, we unravel a clear spatio-temporal relation between latest Cretaceous–Early Cenozoic subduction at the northern edge of the Australian plate, Early Cenozoic Australian plate motion changes and Cenozoic topography evolution of the Australian continent. We present evidence for a ∼4000 km wide subduction zone, which culminated in ophiolite obduction and arc-continent collision in the New Guinea–Pocklington Trough region during subduction termination, coinciding with cessation of spreading in the Coral Sea, a ∼5 cm/yr decrease in northward Australian plate velocity, and slab detachment. Renewed northward motion caused the Australian plate to override the sinking subduction remnant, which we detect with seismic tomography at 800–1200 km depth in the mantle under central-southeast Australia at a position predicted by our absolute plate reconstructions. With a numerical model of slab sinking and mantle flow we predict a long-wavelength subsidence (negative dynamic topography) migrating southward from ∼50 Ma to present, explaining Eocene–Oligocene subsidence of the Queensland Plateau, ∼330 m of late Eocene–early Oligocene subsidence in the Gulf of Carpentaria, Oligocene–Miocene subsidence of the Marion Plateau, and providing a first-order fit to the present-day, ∼200 m deep, topographic depression of the Lake Eyre Basin and Murray–Darling Basin. We propound that dynamic topography evolution provides an independent means to couple geological processes to a mantle reference frame. This is complementary to, and can be integrated with, other approaches such as hotspot and slab reference frames.