Australia's hopes at the Wanderers - and potentially for their home summer - took a major blow in the first session of the match when Shane Watson left the field with an injury to his right hamstring. The loss of Watson followed Australia's decision to send the fast bowler Ryan Harris home due to a hip problem, which will place him in doubt for the first Test against New Zealand.
Arguably Australia's most important player, Watson left the field after bowling the fifth ball of his fourth over, having already made a breakthrough when he had Jacques Rudolph caught behind. It was not immediately clear how serious the injury was, but Watson's history with hamstring complaints meant it was unlikely the Australians would risk him doing any further damage by bowling again in the match.
Watson returned to the field later in the day and stood at first slip - he didn't bowl again - and at the end of the day he was padded up ready to open the innings. However, the ICC's new law forbidding runners means that Watson's impact could be limited by how quickly he can make it to the other end of the pitch.
While Watson is key to Australia's setup due to his all-round abilities, the team is also without Harris, the best bowler in the side. Harris was ruled out of the Test, allowing the 18-year-old Pat Cummins to make his debut, and he was set to return to Australia immediately.
"Ryan Harris had some right hip pain after the first Test in Cape Town," Australia's physio, Alex Kountouris, said. "He was still experiencing pain bowling during the team training session on Wednesday and has therefore been ruled out of the second Test.
"He has had a number of investigations since arriving in Johannesburg that have at this stage excluded serious injury, however he will need to return to Australia for further assessment and to commence his recovery. His return to cricket will be guided by the improvement we see over the next week."
That timeframe does not bode well for his availability for the New Zealand series, which begins at the Gabba in a fortnight. Harris, 32, has been Australia's best bowler since he made his Test debut in New Zealand early last year, easily topping the frontline bowling averages during that period with 35 victims at 21.37.
However, Australia's concern is that Harris has played only half the Tests during that time. He was sent home from the Pakistan series in England last year with a knee injury that required surgery, he suffered a stress fracture in his left ankle during the Boxing Day Ashes Test last year and again needed an operation, and he missed the final Test in Sri Lanka in September due to a hamstring strain.
Three Tests is the most he has strung together in a row. The injuries to Harris and Watson leave Australia with some serious concerns ahead of the New Zealand series and the four-Test series against India that follows.
Harris was to be accompanied on the plane home from South Africa by the left-arm spinner Michael Beer, who the selectors felt would benefit from match-time back home. Trent Copeland and David Warner have remained with the squad but with an Australia A match against New Zealand set to begin next Thursday, it is not out of the question that one of them could be sent to take part in that match.