Australia, led by in-form skipper Michael Clarke's unbeaten 224, reached stumps at 482 for five on a day the world number one Proteas will want to forget.

The South Africans lost paceman Vernon Philander with a back problem before the start of play.

Their problems were then compounded by hamstring injuries to Jacques Kallis and Dale Steyn, leaving their bowling attack at the mercy of the rampant Australian batsmen.

Philander and Kallis went for scans, while pace spearhead Steyn returned to the field after treatment on a tight hamstring.

"Losing Jacques to a type of injury he has never had in his career was a tough one," Kirsten said.

"He has gone for a scan so we don't really know, we will just have to wait for that. He was a little bit sore and I think he made a wise decision, as soon as he felt a twinge he got off the park quickly.

"Obviously from a batting perspective he is going to be important, and these days we don't have runners so it's going to be important that he can bat for us."

Kirsten said Philander, who woke up on match morning with a stiff lower back, hoped to be right for next week's third and final Test in Perth.

The coach said after a long year in which South Africa reached the top ranking with a series win in England the players need time off after last week's drawn Brisbane Test.

"We had four great days of prep leading into this game but it's always a thing that will come up," he told reporters.

"Often when we're home for a Test series we send players home and they come back two days ahead to prepare. There's no exact science to it. You can always find a way to criticise in some department.

"But we've had a long year and we know we had back-to-back Test matches -- second and third Tests coming up -- so we didn't feel four days off was too much to give to the players. They put in hard yards for us this year."

Kirsten said the team had two big days of training coming into the Adelaide Test.

"Every team goes through injuries at some point in time. I don't think we're unique to that," he said. "The fact that it happened on one day, I certainly don't have the answers to that. It was unfortunate."