Abstract Rainfall peaks during austral summer in southern Africa, where most countries are vulnerable to hydroclimate extremes induced by El Niño‐Southern Oscillation (ENSO). Climate models have struggled to simulate the ENSO impact pattern, with excessive southwestward contraction of El Niño‐induced dry anomalies alongside wet anomalies extending too far into central southern Africa. Here we find that the model inability results from an overly‐shallow mean thermocline in the eastern Indian Ocean (IO) that distorts the ENSO teleconnection. During austral summer, instead of an observed basin‐wide IO response to ENSO, the overly‐shallow thermocline leads to a zonal dipole‐like response pattern. Consequently, during El Niño, anomalous equatorial easterly winds promote an onshore moisture transport and a southward shift of summer rainband, leading to a spurious drying in northeast but wetting in southeast and central southern Africa, respectively. Thus, projection of ENSO‐induced rainfall over southern Africa using models with such bias may carry substantial uncertainty.