Cahill receives one-match ban
Cahill, who was sent off in the Socceroos' first group game against Germany, will miss Saturday's match with Ghana but can return for their final Group D match versus Serbia.
Khune, who was dismissed against Uruguay, must sit out the hosts' last Group A match versus France on Tuesday.
Australia were beaten 4-0 by Germany, with Cahill sent off for a foul on Bastian Schweinsteiger early in the second half.
The absence of Australia's top scorer could see Harry Kewell return after a groin injury to face Ghana in a match they must at least draw to have a realistic chance of progressing.
Khune got his marching orders in South Africa's 3-0 defeat by Uruguay when he brought down Luis Suarez to concede a penalty that resulted in the second goal scored by Diego Forlan.
He ws replaced by back-up keeper Moeneeb Josephs.