The tourists resumed at 3-142, needing a further 168 runs to win and square the series.
Ricky Ponting resumed on 54, hoping for an opportunity to make a match-saving and perhaps career-saving century.
Rain fell all morning at The Wanderers but it stopped around midday local time and the ground staff worked hard to drain the ground.
The forecast for the rest of the day still isn't great, with showers around and bad light a potential problem in the late afternoon.
Captain Michael Clarke is the other unbeaten batsman on one, and the weather means Australia only have a short window to attack if they hope to win.
South Africa recorded an emphatic victory in the first Test in Cape Town last week, meaning a draw will be enough for them to claim the series.