In the south São Francisco craton a circular and 8-m amplitude geoid anomaly coincides with the outcropping terrain of an Archean–Paleoproterozoic basement. Broadband magnetotelluric (MT) data inversions of two radial profiles within the positive geoid and Bouguer gravity anomaly yield geo-electrical crustal sections, whereby the lower crust is locally more conductive (10 to 100 Ωm) in spatial coincidence with a denser lower crust modeled by the gravity data. This anomalous lower crust may have resulted from magmatic underplating, associated with Mesoarchean and Proterozoic episodes of tholeiitic dike intrusion. Long-period MT soundings reveal a low electrical resistivity mantle (20 to 200 Ωm) from depths beyond 120 km. Forward geoid modeling, using the scope of the low electrical resistivity region within the mantle as a constraint, entails a density increase (40 to 50 kg/m3) possibly due to Fe enrichment of mantle minerals. However, this factor alone does not explain the observed resistivity. A supplemented presence of small amounts of percolated carbonatite melting (~ 0.005 vol.%), dissolved water and enhanced oxygen fugacity within the peridotitic mantle are viable agents that could explain the less resistive upper mantle. We propose that metasomatic processes confined in the sub-continental lithospheric mantle foster the conditions for a low degree melting with variable CO2, H2O and Fe content. Even though the precise age of this metasomatism is unknown it might be older than the Early Cretaceous based on the evidence that a high-degree of melting in a lithospheric mantle impregnated with carbonatites originated the tholeiitic dike intrusions dispersed from the southeastern border of the São Francisco craton, during the onset of the lithosphere extension and break-up of the western Gondwana. The proxies are the NE Paraná and Espinhaço (130 Ma, Ar/Ar ages) tholeiitic dikes, which contain (~ 3%) carbonatites in their composition. The occurrence of a positive geoid anomaly (+ 10 m) and pre-tholeiites (age > 138 Ma), carbonatites and kimberlites along the west African continental margin (Angola and Namibia) reinforces the presumed age of the São Francisco–Congo craton rejuvenation to be prior to its fragmentation in the Lower Cretaceous.