Tholeiitic melts from the Bouvet triple junction (BTJ) of rift zones in the South Atlantic are moderately enriched rocks with specific lithophile-element patterns. The high (Gd/Yb)n values (up to 2.5) in some tholeiite compositions suggest the presence of garnet in the mantle source of primary BTJ melts. The high Ni and low Mn contents of the most magnesian olivines determined by high-precision probe microanalysis suggest the presence of pyroxenite, along with typical peridotite, in the melting source. The unusually wide within-sample variation in the proportions of pyroxenitic component in the source region (XPx Mn/Fe = 0–90%) indicates different degrees of mantle heterogeneity beneath the spreading zone. Based on geochemical data, this component is a silica-oversaturated eclogite, reacting with peridotite to form olivine-free pyroxenite in the melting source. This component is probably represented either by subducted and recycled oceanic crust or by fragments of the ancient continental lithosphere buried into the mantle after the Gondwana breakup. The observed global and local mantle heterogeneities might have been developed during the complex geodynamic evolution of the Southern Ocean, whose opening was affected by the activity of the Mesozoic Karoo–Maud–Ferrar plume and multiple jumps of the spreading axes, which led to the involvement of fragments of the early oceanic lithosphere in the melting process.