The deep crust of the southernmost margin of Africa contains unresolved tectonic features such as the Paleozoic Cape Fold Belt (CFB), the Paleozoic-Mesozoic Karroo Basin and the largest terrestrial magnetic anomaly, the Beattie Magnetic Anomaly (BMA). Without resolving these structures, our understanding of the evolution of the southern margin will be incomplete and limited. Under the auspices of the Inkaba yeAfrica framework, several geophysical datasets were acquired from 2004 to 2007, along two transects, across the margin and its unique tectonic features. This research presents a tectonic model and crustal geometry, at the centre 100 km of the western transect. The model is derived from the joint interpretation of: surface geology, aeromagnetic data, nearby deep boreholes, teleseismic receiver functions, impedance spectroscopy measurements on borehole samples, near vertical reflection seismic data (NVR), shallow P- and S-wave velocity data, wide angle refraction data and magnetotelluric data. The model differentiates a four component ~42 to 45 km thick crust and constrains the two part BMA to a ~10 to 12 km wide northern zone, and a ~5 to 7 km wide southern zone, both at ~7 to 8 km below surface, continuing for a depth of ~5km, and, contained in the Mesoproterozoic Namaqua-Natal mid-crust. The BMA source is interpreted to be a Namaqua-like massive to disseminated, deformed/metamorphosed strataform sulphide ore body. The model presents evidence in support of a thin-skinned tectonic thrust model for the evolution of the flat-based CFB and shows no significant fore-deep stratigraphic thickening in the Karroo Basin towards the CFB front. The tectonic model suggests a Meso-Proterozoic collision orogen setting, overprinted by a mid-Phanerozoic thin-skinned fold and thrust belt coupled to the far-field accretion/subduction margin to the south.