Neogene collision between Australia and the Banda Arc modified two adjacent depocentres within Australia's North-West Shelf, the Browse and Bonaparte Basins. We identify two components of this modification: (1) continuous long-wavelength amplification of Permo-Carboniferous basement topography, and (2) flexure and normal faulting of Triassic-Recent sedimentary cover. Although this deformation was continuous across the Browse and Bonaparte Basins, the degree of basement architectural control, mechanisms of fault linkage and distribution of syntectonic accommodation space varied significantly between the two basins. These variations reflect fundamental differences in the structural relief, amplitude and depth of rifted basement on either side of a rupture-barrier-style accommodation zone, the Browse/Bonaparte Transition. This long-lived architectural divide, of which there is no discrete structural expression, was amplified by Neogene collision. We examine tectonic rejuvenation of the Browse/Bonaparte Transition and describe a mechanism for actively sustaining long-lived segmentation of the continental shelf.