The Kaizer Chiefs star is nursing a shoulder complaint but insists he will be ready to captain the country in the must-win Group D clash at Soccer City.
Bafana are without regular skipper Thulani Hlatshwayo through injury, with Cape Town City defender Robyn Johannes called up as his replacement.
Mamelodi Sundowns centre-back Motjeka Madisha has also been roped in after FIFA upheld a two-game ban for Chiefs' Erick Mathoho.
“I will be fine for the match,” said Khune after a training session.
“It’s a very important game for all of us and we need all the players fit to go compete and make the country proud. I am struggling with my shoulder but the medical teams from my club and Bafana Bafana are taking good care of it and I am feeling much better.”
Khune is confident Bafana can respond after back-to-back defeats to Cape Verde and revive hopes of earning a spot at Russia 2018.
“What’s important is for us to apply a positive mind to the game, and it’s up to us to get a good result on Saturday so that we can get the full support of the country. When the results are not coming I don’t blame them [the public] for hammering us, we have to deliver. With the crop of players that we have, we are talented and sometimes we don’t realise it, so it’s important that we realise how talented we are and we need to move the country forward with some positive results.”
Stuart Baxter's side are bottom of the pool with a one point from three games - fives points shy of the pace-setting Burkinabe.