Rabada stormed down the pitch in Smith's direction after the LBW dismissal, screaming in his face while making physical contact.
Rabada entered this series with an ominous two-Test ban hanging over his head.
He will appear before a hearing tonight.
Smith and Shaun Marsh steadied temporarily in a 44-run stand before Rabada removed them both lbw. The only thing that will have disappointed them would have been the fact that the Australian tail was again able to wag to some extent with the last 3 wickets contributing the 73 runs that were scored after the tea interval.
Going into Saturday's play in Port Elizabeth - only the seventh day of play inn the series‚ one of which lasted only 22 balls - Crowe has already punished Nathan Lyon‚ David Warner and Quinton de Kock for infractions of discipline.
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The European Commission raised the prospect that Mr Trump could also consider exempting the EU's 28 member states. Amid the uncertainty, today's event was initially left off Thursday's White House public schedule.
Fast bowler Kagiso Rabada was responsible for that big comeback, taking three wickets in the space of two overs just before tea.
Wary of Rabada's disciplinary record and his proximity to another suspension, Smith said at the start of the series the Australians might try to "fire up" the right-armer to see if he would make another mistake.
Rabada had words with Smith after dismissing him leg before wicket and the pair brushed shoulders as Smith headed towards the dressing room.
"I haven't read it", Lyon said, adding he wasn't aware there was a message. His victims included the prize wicket of David Warner for 63. He didn't manage that, but 11 balls later bowled Mitchell Starc. Mitchell Marsh was caught behind for four, Pat Cummins' castle was destroyed first ball, and Mitchell Starc was bowled for eight. You really just never know.