Cameron Bancroft was able to make a significant impact with the bat as the underfire opener showed serious poise before falling on 77 runs.
It was then Nathan Lyon who played the role of saviour for the Aussies as he set a new career high by piling on 47 runs from 38 deliveries.
Kagiso Rabada, Morne Morkel and Vernon Philander toyed with the Australian batting attack as they had the ball moving all over the pitch.
Here are the main talking points from the second day's play in Cape Town.
WARNER INVOLVED IN SPAT WITH FAN
David Warner hasn't been able to escape the controversial spotlight since this series has started and he was in the thick of it again on day two.
After being dismissed by Kagiso Rabada, Warner began the long walk off of the ground and as he approached the gate to start heading up the stairs, he was met by an unruly fan.
Clapping as Warner drew closer, the fan clearly had some choice words to say to the Australian opener which didn't sit kindly with him.
Turning back to face the fan, Warner exchanged a few words before security stepped in and poorly attempted to stem the flow of chatter.
As Warner made his way up the race, the fan kept up alongside him and the men continued chatting all the way up the stairs.
Australian security officer Frank Dimasi then stepped out of the dressing room and jumped the fence before having a conversation with the fan.
The fan was later evicted, along with several others, from the Newlands stadium after the altercation. He is believed to be a member of the Western Province Cricket Club and could yet face further punishment from the group founded in 1864.
Controversy has followed Warner during his time in South Africa, most notably when he clashed with Quinton de Kock after the wicketkeeper hurled "vile and disgusting" remarks in his direction about his wife Candice.
A tantalising series has often played second fiddle to the constant string of controversies and the latest involving Warner threatened to steal more shine.
Australian coach Darren Lehmann labelled the abuse directed towards his players as "disgraceful" and stated Cricket Australia had lodged a complaint to Cricket South Africa.
ELGAR & SMITH ENTER RECORD BOOKS
South African opening batsman Dean Elgar equalled a world record when he carried his bat through a completed innings for the third time as his team were bowled out for 311 on the second day of the third Test against Australia on Friday.
Elgar finished unbeaten on 141 — only Desmond Haynes of the West Indies had previously batted unbeaten through a Test innings on three occasions.
Elgar and Kagiso Rabada frustrated the Australians for 50 minutes as they took South Africa's overnight total from 266 for eight. They shared a partnership of 50 before off-spinner Nathan Lyon had Rabada caught by Smith at slip off his first ball of he day.
Morne Morkel hit a four before falling in identical fashion four balls later. Elgar batted for 434 minutes, faced 284 balls and hit 20 fours and a six.
After starting his Test career with a pair of ducks in 2012, against Australia, Elgar has grown into one of South Africa's batting stalwarts.
Australian captain Steve Smith also equalled a world record when he caught South Africa's last two batsmen for a total of five catches in the innings, the joint most by a fielder.
Although ten other fielders shared the record, Smith was only the second Australian to achieve the feat after Vic Richardson in 1935/36.
HEAT BUILDING ON KHAWAJA
Usman Khawaja has been under immense pressure during the current series and after another dismal showing with the bat, he'll be praying to retain his place in the side.
He strolled out to the crease after Warner had lost his battle against Kagiso Rabada and with the Australians needing a steading partnership.
For reasons unknown, Khawaja didn't seem interested in sticking around at the crease and he played a bizarre shot off the bowling of Morne Morkel.
Khawaja hooked a mid-length delivery around the corner and into the waiting hands of Rabada to end his innings after contributing only five runs.
So far during the series Khawaja has scored a total of 104 runs from five innings. That total includes his 75 during the second innings of the Test in Durban.
Which means from his other four times at the crease, he has compiled only 29 runs. For player coming in at first drop, the recent displays simply haven't been good enough.
Khawaja will need a big score during the second innings of this Test or he may face the axe from the selectors.
