Khune's error allowed Buitumelo Sekgobela to tap the ball home, with Chiefs looking a shadow of the side that thumped Orlando Pirates in the Telkom Knockout Final a week ago.
Chiefs did look full confidence early on and passed the ball around nicely but, against all odds, it was the home side that took the lead after Khune’s mistake in the 13th minute.
Mpho Makola fired in a long-range shot that bounced just in front of the Bafana Bafana keeper and seemed to skew of the pitch slightly, resulting in Khune fumbling the ball straight into the path of Sekgobela, who made no mistake.
Sthembiso Ngcobo should have found the equaliser for his side three minutes later, but he squandered a golden opportunity after being played in by Knowledge Musona.
The remainder of the half saw very little goal mouth action at either end. However, that was only until the final minute of the half when Khune probably produced one of the saves of the season.
Sekgobela made a break behind the Chiefs defence and found himself with plenty of time and space, but Khune was in no mood to concede a second goal and did brilliantly diving full stretch to his left to deny Sekgobela.
The second half saw a predictable pattern emerge as Chiefs produced attack after attack in search of the equaliser, while Stars seemed content to sit back in defence and hit on the counter-attack.
Ngcobo came close to scoring five minutes into the half when he got off a shot from the edge of the 18-yard area, but his effort just skimmed the wrong side of the upright.
Ten minutes later and it was Musona who missed a golden scoring opportunity when he headed over from only six-yards out when he should have done a lot better.
In the end Chiefs, despite their domination of the second half, couldn’t break the down the stubborn Free State Stars defence.