Bad light brought a premature end to the day after 83 overs bowled with AB de Villiers not out on 51 and JP Duminy on two at the close.
De Villiers passed 7,000 test runs and became the first player in history to score half-centuries in 12 tests in a row.
It might well have been a better day for the hosts after they won the toss and elected to bat, but Dean Elgar (83) and debutant Quinton de Kock (seven) gave their wickets away with rash shots.
The pitch did not have the devil of Pretoria and rendered Mitchell Johnson less effective, the South Africans playing him with relative comfort once the shine had been taken off the new ball.
"This is probably the slowest I have ever seen the pitch in Port Elizabeth," Elgar told reporters.
"Here patience is one of the key things teams look for. I knew I had to bat long to put us in a good position, first- innings runs here at St George's are golden."
It has been a bitter-sweet week for Elgar, who found out he would play in this test match on the same day Cricket South Africa decided not to renew his central contract.
"I got the bad news first, then they softened me up with the good news," he said.
Proteas captain Graeme Smith (nine) said at the toss his side wanted to bat first and put Australia under pressure, but it was South Africa who felt the early heat.
Smith was struck on the back leg by Ryan Harris with the total on 10 and the umpire had no hesitation in giving him out lbw. In the next over, Johnson breached the defence of Hashim Amla who was also trapped leg before for a duck.
But Elgar and Faf du Plessis (55) batted patiently for a third-wicket partnership of 112 before the latter gave a catch to Steve Smith at short leg off the bowling of Nathan Lyon.
Left-handed opener Elgar, brought back into the side for the sick Alviro Petersen, added a further 58 with the fluent De Villiers before he tried to smash Lyon to the boundary and skied the ball to Ryan Harris at mid-off.
That brought De Kock to the crease one place higher than expected, with Duminy slipping down to seven, and the confident 21-year-old got off the mark in test cricket with a boundary.
But the brashness of youth got the better of him and presented with the part-time leg-spin of Smith, he too tried a mow the ball over the boundary but succeeded only in lofting it to substitute fielder Moises Henriques at mid-off.
Lyon (two for 47) was the pick of the Australian bowlers, while Johnson, so ferocious in the 281-run victory in the first test in Pretoria, managed just a single wicket at a cost of almost three runs an over.
"We thought it was a good day on a slow pitch, our quick bowlers put in a fantastic effort, the energy they showed was brilliant," Lyon said.
"We must take the new ball tomorrow and get the last five wickets and let our batters have a crack.
"There was not much going on [with the pitch], even with the new ball, so we need to bowl with patience and build pressure. Test cricket is all about patience, it's a mental game, we need to make sure we outlast the opposition."
