Tim Paine, however, frustrated the home side by scoring 36 runs as Australia added 61 runs for the last two wickets.
At stumps, South Africa were 39-1 after batting through 12 overs at the end of the day, losing Aiden Markram for 11.
Rabada went on to take a further four wickets after seeing off Smith, ending the innings with figures of 5-96. I pulled the guys together, just the playing group, and said let's not let these incidents overshadow the way we played and get in the way of the way we want to play in this series.
Rabada will contest the ban in a hearing after play on Saturday - but in order to avoid a series-ending suspension, he will need to prove the contact was accidental.
He believes that De Kock's response to two hours of on and off field sledging was expected.
James Sutherland, the Cricket Australia chief executive, has put the national team on notice to improve its on-field behaviour, after the CA board discussed the unsavoury events of the Durban Test match.
"I'm pleased with Davey that he stuck his hand up, said he made a mistake and he could handle things better", Smith said.
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The International Cricket Council said that match referee Jeff Crowe will remind the teams of their responsiblities after Australian vice-captain Warner was fined 75 percent of his match fee from the Durban game and the Proteas wicketkeeper/batsman docked 25 percent. "I don't think anyone's read it, to be honest". The ongoing second Test match has been tantalisingly poised and the drama continues to unfold in Port Elizabeth.
Australia won by 118 runs for an early lead in the four-test series.
"After the last game it was always going to be a bit sensitive", Philander said. As matters stand, they are 90 runs adrift of the Aussies.
Warner was out for 63 as South Africa came back with five wickets in the afternoon following a solid opening session for the tourists.
Rabada had words with Smith after dismissing him leg before wicket and the pair brushed shoulders as Smith headed towards the dressing room.
Fast bowler Kagiso Rabada was responsible for that big comeback, taking three wickets in the space of two overs just before tea.