Hlatshwayo has been ruled out of the Bafana squad to face Burkina Faso at FNB Stadium on Saturday because of a knee injury.
The Bidvest Wits skipper has been replaced by Cape Town City defender Robyn Johannes.
“Khune will be the captain if he’s fit to play,” Baxter told the media at a press conference on Monday morning.
On Johannes’ call-up, Baxter said: “Robyn Johannes has been rewarded for the good form he’s shown for his club, last year and this year.”
Bafana are set to take on Burkina Faso in a 2018 World Cup qualifier at FNB Stadium on Saturday.