Seismic‐wave velocities offer essential constraints on the temperature, thickness, and composition of the lithosphere of cratons. We invert broadband, Rayleigh‐wave phase and Love‐wave phase velocities measured across the Kaapvaal Craton and Limpopo Belt for depth distributions of shear‐wave velocity and radial anisotropy, from the upper‐crust down to deep upper mantle. Our probabilistic, Bayesian inversion addresses model nonuniqueness by means of direct parameter‐space sampling. An increase in Vs between the Moho and 100–150 km depths occurs across the region and can be explained by the gradual emergence of garnet below 80 km, due to the spinel peridotite‐garnet peridotite transformation and due to the exsolution of garnet from mantle orthopyroxene. Lateral variations in this Vs gradient can provide new information on lateral compositional variations. Cold cratonic lithosphere is manifest in very high shear velocities, up to 4.8 km/s. The depth extent of the shear‐velocity anomaly and the inferred lithospheric thickness increase from ∼200 km beneath the central and southwestern Kaapvaal to ∼300 km beneath the Limpopo Belt. Curiously, surface elevation decreases monotonically with the increasing lithospheric thickness. The relationship between the lithospheric thickness and topography depends on the lithospheric composition and, with the crustal structure taken into account, our results imply that the bottom part of the Limpopo lithosphere (200–300 km) is weakly‐to‐moderately depleted (Mg# 89.7–90.8). Our results also show that the central‐southwestern Kaapvaal lithosphere is thinner than it was (according to kimberlites) 100–200 m.y. ago. It may have been thinned by the same mantle plume that, initially, triggered the kimberlite eruptions.