The announcement was made on Tuesday at the squad’s base camp in Durban.
Thulani Hlatshwayo, Dean Furman and Hlompho Kekana have been appointed as vice-captains.
Khune is the captain of Kaizer Chiefs, while the trio of Hlatshwayo, Furman and Kekana hold leadership positions at Bidvest Wits, Supersport United and Mamelodi Sundowns respectively.
All have worn the Bafana Bafana armband with the exception of Kekana.
Both Khune and Hlatshwayo have been alternating as captains in the Bafana set-up over the past few months.
Bafana Bafana face Guinea-Bissau at Moses Mabhida Stadium in Durban on Saturday at 15:00 while their next fixture will be against Angola three days later (Tuesday, March 28 at Buffalo City Stadium in East London at 19:00.
Owen da Gama will serve as caretaker coach.