Khune only played 10 minutes of the practice match as he limped off at Milpark Stadium.
However, the 29-year-old says the knock is of minor concern.
"Nothing serious good people. i'ts just a bruise but I will be OK," Khune said on Twitter.
Khune has been included in the national U-23 squad for next month's Olympics as an overage player, along with clubmate Erick Mathoho.
The Amakhosi pair are scheduled to first play in the Carling Black Label Champion Cup against Orlando Pirates at FNB Stadium on July 30.