Amla surpassed 5,000 career runs and shared partnerships of 136 with Jacques Kaliis (84 not out) for the third wicket and 90 for the second wicket with opener Alviro Petersen (64).
A leaked Australia team dossier which appeared in local media in the lead-up to the first Test said Amla was susceptible to "psychological warfare."
There was no indication of any such weakness today as he moved within ten runs of posting a century for a third successive Test against Australia.
He did give some chances and half chances, including a slashing edge between wicketkeeper and first slip off Nathan Lyon when he was on 62, but remained composed.
The 63-Test veteran went in at the dismissal of skipper Graeme Smith (10) with the total at 29. He survived an appeal for lbw before he'd scored and a caught-and-bowled chance to Peter Siddle on 74. He had faced 205 balls and stroked six boundaries and a six when play was halted eight overs early due to bad light.
Kallis plundered the attack for eight boundaries and a six from the 136 balls he faced.
For all the speculation of aggressive pace dominating in conditions aiding swing and seam, the Australian attack toiled without much success on a green-tinged Gabba wicket.
Siddle was frustrated after missing opportunities to break up the Amla-Kallis partnership, which has produced some outstanding 100-plus stands in Test cricket.
Kallis got a reprieve when he was on 42 and the total at 192-2 when he started walking after miscuing a Siddle slower ball and looping a catch to Lyon at mid-off. Umpire Asad Rauf told Kallis to wait while he checked for a no-ball, which TV replays confirmed, showing no part of Siddle's front foot behind the crease at the point of delivery. Siddle missed another chance in the 62nd over when he couldn't grasp a driven return catch from Amla. South Africa was 206-2 at the time.
Earlier, Petersen also had a let off, getting the benefit of the doubt when Australia referred a not out decision to the TV umpire for an lbw appeal by Ben Hilfenhaus. The ball pitched just outside the line and appeared to hit in front, on Petersen's front toe, when he was on 51.
Petersen hit two more boundaries before mistiming a Lyon delivery to Mike Hussey at mid-on, leaving South Africa at 119-2.
Skipper Smith didn't get any second chances after winning the toss and batting, becoming the first South Africa batsman dismissed in a test at the Gabba ground in 49 years when he was trapped lbw by James Pattinson in the 11th over.
He was initially adjudged not out by umpire Billy Bowden despite being hit on the back pad, directly in front of the stumps, but the decision was overruled on review.
Showers or storms were forecast for today and tomorrow, but there was no rain during the first 82 overs despite the gloomy conditions which finally caused an early end to play. South Africa, playing its first test at the Gabba since 1963, went in with five pace options after selecting seamer Rory Kleinveldt to make his debut at the expense of legspinner Imran Tahir.
Kleinveldt will supplement the world-class pace trio of Dale Steyn, Vernon Philander and Morne Morkel, and veteran allrounder Kallis.
Petersen survived a strong appeal and a review by the TV umpire on an lbw decision on 51, then mis-timed an attempted shot through mid-wicket off Nathan Lyon and was caught by Mike Hussey for 64.