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The Bidvest Wits skipper has been replaced by Cape Town City defender Robyn Johannes.
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“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.
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