But they hadn't counted on keeper Tim Paine's rearguard action for the fourth section. With his remaining ball in the over, Rabada had Pat Cummins caught behind to be on a hat-trick.
Smith had raised eyebrows at the toss with his decision to bat in what were clearly bowling conditions but stated that if the batsmen could get through the first hour a big first innings score is on the cards.
But on the field, South Africa only strengthened their already good position in the second Test in Port Elizabeth, adding 71 runs for the loss of just a single wicket - that of Rabada, the nightwatchman.
Smith, who unsuccessfully reviewed after being trapped lbw on 25, looked decidedly unimpressed with the physical contact. But the second day starts with South Africa just 204 runs behind with plenty of firepower left in their batting line up.
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.
Warner ahead of second Test has mentioned that he is ready to break ice with de Kock after his Durban spat.
Sutherland's message, however, hadn't been digested by the Australian players.
"We're pretty comfortable with where we're sitting", Lyon said. "I don't think anyone's read it, to be honest".
South Africa player De Kock was also reported along with Warner for the incident.
"It's that type of wicket where you actually probably never feel like you're in", Lyon said.
Warner (63 off 100 balls, 9 fours) was the only Australian batsman to get past 50.
After Warner's departure South Africa came back with five wickets in the afternoon following a solid opening session for the tourists.
But everything changed when Rabada returned to the attack.
Tea was taken after Mitchell Marsh was out. He didn't manage that but 11 balls later he bowled Mitchell Starc.