The hosts declared on 480/7.
Hashim Amla (25*) and JP Duminy (2*) are the overnight batsmen, following the dismissal of Alviro Petersen, who was caught off a leading edge for 38.
Skipper Graeme Smith scored a brisk 60 off 84 balls, after which he retired, as he looked to give the rest of the line-up opportunities.
Australia A's batsmen added 155 runs to their overnight score, with Alex Doolan finishing unbeaten on his highest first-class score of 161.
Doolan and Tim Paine partnered in a record 162-run eighth-wicket partnership, in tough bowling conditions.
"All our seamers got a bowl and Imran (Tahir) got a long bowl, which is exactly what we wanted, so everything has been good," Hashim Amla said after the day's play.
Smith used his pace bowlers sparingly and strategically, as his arsenal continues with the necessary preparation ahead of Friday's opening match.
Vernon Philander bowled 21 overs without a wicket, an uncommon statistic but one that doesn't bother the Proteas.
"He bowled really well up front," Amla said.
"On any other day he could have picked up a five-for. I know with him it is about sticking to his processes and the way he bowled today is as well as we have seen him."
The rest of the batters will be looking to capitalise on some middle time with AB de Villiers, Jacques Rudolph and Faf du Plessis the main batsmen to come.
"Time in the middle is invaluable, no matter what the state of the wicket," Amla continued.
"Graeme (Smith), Alviro (Petersen) and I would without a doubt take the middle practice over a net practice.
"There is no practice like match practice and fortunately it has been good for us."
One of the highlights of the day was Amla's rare four-over spell of off-spin, which he was openly delighted about.
"I enjoyed the four overs," Amla – who has one first-class wicket to his name – added.
"I've been in the captain's ear a few times and fortunately the time came for me to show my skill, it didn't go too badly." – Sapa