Khune starred against the Burkinabe, setting up two goals from behind a defence that featured debutant Thamsanqa Mkhize, SuperSport United centre-backs Morgan Gould and Clayton Daniels, and left-back Sifiso Hlanti.
Bafana were without regular defensive starters Thulani Hlatshwayo, Erick Mathoho and Ramahlwe Mphahlele through a combination of injury and suspension.
Khune says work on the training ground paid off against the Stallions as Stuart Baxter's men kept alive their hopes of qualifying for the World Cup.
Khune said: "I've played with Morgan at club level and I've played with Clayton at international level. Under coach Stuart Baxter, since I've been training, communication we have been doing the whole week.
"We told ourselves let's give the same commitment and take the same confidence into the match and it worked. Yes, I've played under a lot of defensive players, but with good communication everything just falls into place.
"With Mkhize, we've been helping him. He is very quiet, he is not talkative. But he listens and whenever we give him instructions he listens and goes into positions. He played very well and we all congratulated him on his first match for Bafana," concluded the Kaizer Chiefs star, who sprained an ankle on the weekend.
Bafana must beat Senegal on 10 and 14 November to earn a berth at Russia 2018.