“She has decided to focus on the 800m,” Verster said on Friday, though he would not elaborate on the decision.
Semenya, the former 800m world champion and London 2012 silver medallist in the two-lap event, had qualified for the 400m, 800m and 1 500m contests at the Rio showpiece.
She had already confirmed she would not compete in the 1 500m race, and Verster had said she had been entered in the 400m but would make a decision closer to the Games.
In spectacular form this season, she set a national record of 1:55.33 at the Diamond League meeting in Monaco last month, establishing her place as the favourite for 800m gold at the multi-sport showpiece.
The Rio Olympics officially started with the opening ceremony on Friday night, and the athletics competition begins on August 12.