Archean cratons, and the stitching Proterozoic orogenic belts on their flanks, form an integral part of the Southern Africa tectonic landscape. Of these, virtually nothing is known of the position and thickness of the southern boundary of the composite Congo craton and the Neoproterozoic Pan-African orogenic belt due to thick sedimentary cover. We present the first lithospheric-scale geophysical study of that cryptic boundary and define its geometry at depth. Our results are derived from two-dimensional (2-D) and three-dimensional (3-D) inversion of magnetotelluric data acquired along four semiparallel profiles crossing the Kalahari craton across the Damara-Ghanzi-Chobe belts (DGC) and extending into the Congo craton. Two-dimensional and three-dimensional electrical resistivity models show significant lateral variation in the crust and upper mantle across strike from the younger DGC orogen to the older adjacent cratons. We find Damara belt lithosphere to be more conductive and significantly thinner than that of the adjacent Congo craton. The Congo craton is characterized by very thick (to depths of 250 km) and resistive (i.e., cold) lithosphere. Resistive upper crustal features are interpreted as caused by igneous intrusions emplaced during Pan-African magmatism. Graphite-bearing calcite marbles and sulfides are widespread in the Damara belt and account for the high crustal conductivity in the Central Zone. The resistivity models provide new constraints on the southern extent of the greater Congo craton and suggest that the current boundary drawn on geological maps needs revision and that the craton should be extended further south.