Rabada went on to take four more wickets, claiming five in the space of 18 balls, either side of the tea interval, to scythe through Australia's middle order.
Smith and du Plessis met with match referee Jeff Crowe on match eve, with both captains expressing hope this game will be played in better spirits than the acrimonious first Test.
The incident happened after Rabada scalped Smith's crucial wicket for 25 and celebrated the victory by brushing his shoulder against the departing skipper.
The speedster was given three demerit points for "inappropriate and deliberate physical contact" in 2017, having brushed Niroshan Dickwella when the Sri Lankan was running between the wickets.
Rabada is already sitting on 5 points and an additional 3-4 would result in a two-Test suspension, ruling him out of the rest of the series.
Rabada now has five demerit points to his name, having picked up a third sanction by the ICC in the past 12 months with his send off of India's Shikhar Dhawan in the fifth match of their one-day series last month.
Rabada takes 3 quick wickets to leave Australia reeling
Rabada has contested the charge on the basis of unintentional contact.
Rabada was noticeably reserved in the volatile first Test, with Proteas paceman Dale Steyn suggesting he was toning down his aggression because it the threat of being banned. "I have spoken to him a few times about it, to try and get him to relax a bit", Holding told ESPNcricinfo.
Ravi, the designated television match official, was on the field with New Zealand umpire Chris Gaffaney feeling unwell.
"He would leave a massive hole, he's a big part of this bowling line up".
He would be the third player to receive punishment in the tempestuous test series so far, with David Warner (three points) and Quinton de Kock (one) each sanctioned for a verbal spat at tea on the fourth day of the first test.
Smith, Nathan Lyon and Josh Hazlewood all gave the fast bowler a vocal welcome.More news: 'Flippy' the burger-flipping robot is taken offline after just one day
More news: White House aid Conway launches first wave in final Pa. congressional push
More news: Mohammed Shami-Hasin Jahan saga: NCW assures help to cricketer's wife