Boland, selected in Gqeberha as Australia omitted off-spinner Nathan Lyon and went in with a four-pronged pace attack, bowled Aiden Markam (11) off an inside edge in the ninth over before then nicking off David Bedingham (0) with his next delivery.
South Africa, 1-0 down in the three-match series after a 214-run defeat in the opening game at Durban, were 12-2 at that stage having been put into bat but reached the premature stumps without any further casualties as debutant Marques Ackerman (5no off 32 balls) and captain Temba Bavuma (4no off 13) battled.
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Rain meant play started two hours later than scheduled and it returned to bring about an early lunch after just 5.3 overs before another downpour led to the day being abandoned at 4.15pm local time at St George’s Park.
Boland for Lyon was Australia’s only change from the first match, with the Baggy Greens leaving their premier spinner out of a red-ball Test in which he was fit to play for the first time since 2013.
South Africa made three alterations with left-arm spinner Keshav Maharaj, wicketkeeper Kyle Verreynne and batter Tristan Stubbs axed for batters Ackerman and Matthew Breetzke and fit-again paceman Kagiso Rabada.
Ryan Rickelton took the wicketkeepjng gloves in Verreynne’s absence and dropped down from his opening position to No 6, with Ackerman coming in to partner Markam at the top of the order.
Ackerman, 30, was opening in a first-class match for the first time and dug in on a seam-friendly wicket.
Watch day two of the second Test between South Africa and Australia live on Sky Sports Cricket from 8am Monday. Not got Sky? Latest Sky Sports deals or stream with no contract on NOW.
