The East African Rift System (EARS) provides a unique location for exploring factors influencing the development and maturation of continental rifting. In particular, the geographical relationships between Cenozoic rifts and Pre‐Cambrian lithospheric structures suggest that such preexisting structures exert an influence on early‐stage rift geometry and behavior. This study uses Rayleigh wave phase velocity at periods of 20 to 100 s to study lateral variability in the lithospheric structures of rift segments and preexisting structures in the central and southern EARS. The model is constructed using records of 789 earthquakes, recorded by a composite station array of 235 stations from nonconcurrent seismic networks between 1994 and 2015. In the central EARS, we observe fast velocities beneath the Tanzania Craton, isolated low‐velocity regions along the Western Rift Branch, and low velocities in all resolved portions of the Eastern Rift Branch, consistent with previous regional surface wave studies. South of the Tanzania Craton, we observe linear low‐velocity zones trending both southeast and southwest from the Tanzania Divergence Zone, suggesting a southern bifurcation of the Eastern Rift Branch. In the southern portions of the Western Rift Branch, the Malawi Rift borders fast velocities associated with the Bangweulu Block and Irumide Belt. Anomalously fast velocities in these regions persist to long periods, confirming the existence of cratonic lithosphere inferred from previous studies. Fast velocities observed beneath the Irumide Belt extend across the southernmost portion of the Malawi Rift, suggesting that strong lithosphere in this region may hinder the southern propagation of the rift.