The Group D game kicks off at 19h00.
Kaizer Chiefs keeper Khune suffered a facial fracture in a Telkom Knockout tie against Chippa United last Sunday, but has been cleared to oversee the back four of Clayton Daniels, Morgan Gould, Thamsanqa Mkhize and Sifiso Hlanti.
The midfield consists of Dean Furman, Themba Zwane, Sibusiso Vilakazi and Kamohelo Mokotjo.
Lebogang Manyama will partner Percy Tau upfront.
Baxter is without injured skipper Thulani Hlatshwayo and the suspended Bongani Zungu, while fellow midfielder Hlompho Kekana has been excused from international duty due to a family tragedy. His Mamelodi Sundowns teammate Tiyani Mabunda was consequently drafted into the Bafana squad.
Holland-based playmaker Thulani Serero refused to honour a call-up unless he was guaranteed game-time, according to Baxter.
Baxter's men must win in Polokwane and in the rematch in Dakar on Tuesday to book a spot at Russia 2018.
Bafana XI: Khune, Daniels, Gould, Mkhize, Hlanti, Furman, Mokotjo, Manyama, Zwane, Vilakazi, Tau.
Substitutes: Wayne Sandilands, Ronwen Williams, Motjeka Madisha, Tebogo Langerman, Erick Mathoho, Siphiwe Tshabalala, Phakamani Mahlambi, Tiyani Mabunda, Keagan Dolly, Bradley Grobler.