Khune sustained the blow in Chiefs' 1-0 win over Chippa United in the Telkom Knockout quarter-finals in Port Elizabeth on Sunday following a collision with Kurt Lentjies.
The in-form shot-stopper was stretchered off the park at Nelson Mandela Bay Stadium as defender Daniel Cardoso saw out the closing stages in goal for the Glamour Boys.
Chiefs later posted an update on Khune's condition on Twitter, saying: "Injury Update: Captain Itu has a fracture to a bone in his face. He will see a specialist regarding this and we will update you after."
Orlando Pirates' Wayne Sandilands and SuperSport United's Ronwen Williams are the other two keepers in Bafana coach Stuart Baxter's squad.
Bafana will host the Teranga Lions at Peter Mokaba Stadium (19h00) before contesting the rematch four days later in Dakar at Stade Leopold Sedar Senghor (21h30 SA time).
Baxter's men must win both remaining Group D ties to book their ticket to Russia 2018.