Semenya, clocking an unofficial time of 2:04.13, took the lead from the start of the two-lap race in north-west university town Potchefstroom during the first meeting in a national athletics series.
The 20-year-old has won three international races since being cleared to compete last year by the International Association of Athletics Federations (IAAF).
Tests into Semenya's sex were announced by the IAAF shortly before the athlete won a gold medal at the 2009 world championships in Berlin, thrusting her into the global spotlight.
Leaked test results said Semenya was a hermaphrodite, sparking anger from the South African public and government.
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