The Olympic and World champion over 800m, Semenya, crossed the line in 49.96 seconds beating Heide Seyerling previous SA record.
Semenya now holds South African records in the 400m, 800m, 1000m and 1500m events.
South African team won another gold on day three at the 21st African championships in the men's 4x100m relay. Akani Simbine, Henricho Bruintjies, Simon Magakwe and Emile Erasmus clocked 38.25 beating Nigeria and Ivory Coast into second and third respectively.