Khune kept a clean sheet as Amakhosi extended their lead at the Absa Premiership summit to 10 points courtesy of Mandla Masango's early strike at FNB Stadium.
However, the former Bafana Bafana number one, who spent months on the sidelines through injury, conceded he still requires further conditioning.
Khune said: "Even the coach said it yesterday, that I was at 95 percent, and I just laughed it off, I thought I was more than that. But it showed tonight that I am not up to the standard I usually am on.
"I will be working hard, and I have been working very hard at training to get my fitness back. With the performance tonight, it shows I am on the right track."
Meanwhile, Khune was naturally pleased Chiefs were able to dispatch the Urban Warriors ahead of Saturday's Soweto Derby with Orlando Pirates.
"We came here as the hosts, we had to pick up the three points. It was very important that we become consistent with nine games to go.
"Saturday's a big one, South Africa will come to a standstill. Everyone is expecting fireworks, and with the performance tonight we showed we are up for the challenge."