Steven Smith tried all of his four main strike bowlers but the only breakthrough came in Pat Cummins' first over, when he had Rabada bowled, chopping on to leave the total at 67 for 2.
Cricket South Africa said Rabada, who devastated the Australian batting order on the first day, has been charged with a level two offence over the altercation.
Match referee Jeff Crowe, having implored both captains to improve the behaviour of their respective sides after handing out three charges in the wake of a spiteful series opener, faces a big decision.
As you can see by watching the various videos below, the fiery South African screamed in Smith's direction 'Yes!
The findings of that inquiry were handed down before play on day two on Saturday, with Rabada hit with a grade two offence for physical contact with the shoulder.
Rabada had words with Smith after dismissing him leg before wicket and the pair brushed shoulders as Smith headed towards the dressing room. Previous year he was found guilty of deliberate physical contact with Sri Lanka's Niroshan Dickwella and was given three demerit points.
Australia won in Durban by 118 runs to lead the four-test series 1-0.
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"He's sat in front of the media and said "yep, you know what I said was either defending my family", like he did in this last one".
"Sometimes there is a fine line whether to celebrate too hard. It's up to the umpires and the ICC match officials to make that call".
"The wicket felt like it had a little bit in it all day and they batted especially well in the second session".
In the second Test South African fans have bumped up their efforts to get under Warner's skin, distributing Sonny Bill Williams masks at Port Elizabeth, a low blow reference to Mrs Warner's intimate pub bathroom encounter with the rugby star in 2007.
Rabada's running battle with the tourists continued when he was sent out as nightwatchman on day one. He didn't manage that but 11 balls later he bowled Mitchell Starc.
Rabada missed the second Test at Trent Bridge as a result; four demerit points lead to a ban of one Test or two limited-overs games, whichever comes first, while eight demerit points result in double the penalty.
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