Semenya won comfortably from Mandie Brandt in hot and windy conditions at Nelson Mandela University in this Indian Ocean city, but her time of two minutes, 02.68 seconds was disappointing.
The 21-year-old, whose triumph at the 2009 world championships in Berlin led to gender tests amid complaints from rivals, bettered the Olympic qualifying time of 1:59.90 when finishing second last year in defence of the title.
But she needs to match or better that time again before June 30 to realise her dream of competing at the quadrennial multi-sport showpiece scheduled from July 27 to August 12 in the English capital.
Semenya, who has recovered from a lower back injury, swapped coaches last year, replacing Michael Seme with 2000 Sydney Olympics 800 metres gold medalist Maria Mutola from Mozambique.
Mutola warned ahead of the national final that any time over two minutes could knock the confidence of her protege, who is considered the best hope of a South African athletics medal at the Games.