However, it was Rabada's dismissal of Australia captain Smith that may land him in hot water with the ICC, as the Proteas paceman gave a screaming send-off and made contact with his opponent's shoulder.
Australia and South Africa get set to take on each other in the second Test of the series.
South Africa were 39 for one wicket in reply at the close, losing Aiden Markram for 11 runs.
Fast bowler Kagiso Rabada was responsible for that big comeback, taking three wickets in the space of two overs just before tea.
Rabada added a fifth wicket in the same spell as Australia were bowled out for 243 after winning the toss and batting on a green-tinged pitch on an overcast day at St George's Park.
In Rabada's case the alleged offence is that of making inappropriate or deliberate contact with another player.
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Australia couldn't do much else in that first hour.
Cummins won an lbw decision against Hashim Amla when the batsman was on seven but the decision, by substitute umpire Sunderam Ravi, was overturned on review when the ball was shown to have struck Amla outside the line of the stumps.
Australia's lead is now 204 runs, with Nathan Lyon insisting they can fight back with the bowl on day two.
Footage of Warner's staircase stoush in Durban took the gloss off Australia's series-opening win and ensured all eyes would be on the vice-captain on Friday. Paine was the last wicket to fall when Ngidi bowled him.
Earlier, David Warner and Cameron Bancroft shared a 98-run stand and did well to see off the new ball in tricky conditions.
Nathan Lyon said he hadn't spoken to Smith. Cummins also edged behind and Starc was clean bowled, with Rabada aiming a comment at the Australian as he went on his way.
But they hadn't counted on keeper Tim Paine's rearguard action for the fourth section.