Smith remained unbeaten on 111 and his opening partner Alviro Petersen made 54 as the Proteas ended the day at 217/2 in 67 overs.
Australia bowlers had only one success through the part-time legspin of David Warner who got Hashim Amla stumped by Matthew Wade. The other wicket was a run out off Petersen.
Earlier, resuming from 482/5, Australia were bowled out for 550 in 107.2 overs. Paceman Morne Morkel took five wickets for 146 runs.
Legspinner Imran Tahir had a forgettable bowling stint in the first innings as he was plundered for 180 runs in his 23 overs without a success. He conceded runs at 7.82 per over.
Australia captain Michael Clarke was bowled by Morkel for 230. On Thursday, Clarke had become the first man in Test history to score four double hundreds in a calendar year.