Kgatlana was named as one of the four players on standby should injury strike at the event, as is now the case.
She and the others - Kaylin Swart (goalkeeper), Nomathemba Ntsibande (defender) and Chantelle Esau (midfielder) - have been training with the team in Brazil in line with tournament rules.
South Africa made a formal request to replace Nongwaya with Kgatlana and it has been approved.
Nongwaya was ruled out of the 2016 Rio Olympic Games due to an ankle injury sustained in the 1-0 loss to Sweden in the 40th minute. Linda Motlhalo replaced her in the match.
South Africa takes on China tonight at the Olympic Stadium in Rio de Janeiro. Kick-off is at 19h00 local time (midnight SA time).