Rabada recovered from an expensive opening spell before lunch to trap Australia captain Steve Smith and Shaun Marsh lbw, before then taking the wicket of Mitchell Marsh at the end of the second session to change the complexion of the contest in the space of two overs.
"CA has reminded the team of the standards of behaviour expected of players representing Australia", he said, pointing to the ICC Code of Conduct and the need to play within the laws and spirit of the game.
Warner was fined 75% of his match fee by the ICC on Wednesday and given three demerit points after video footage appeared to show him being restrained by team-mates during a row with the South Africa wicketkeeper.
"I'm pleased with Davey that he stuck his hand up, said he made a mistake and he could handle things better", Smith said.
"I pulled the guys together and said let's not let these incidents overshadow the way we played".
Mitchell Starc (8) was Rabada's fifth victim, clean bowled to leave Australia reeling on 182-8.
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Rabada was a highlight of the day's play, claiming his eighth five wicket haul in his young career. The match referee Jeff Crowe will hold a hearing after play on day three of the Test.
Captain Smith admitted that most of talking point from the game focussed on the controversy rather than Australia's impressive performance.
After the explosive fallout to the first Test, all eyes were on David Warner and Quinton de Kock as the Aussie opener shaped up to face the first morning against South Africa.
Following Markram's dismissal, Rabada upped the ante as he took the attack to the Australian bowlers during his unbeaten 17-run stand with Dean Elgar before stumps was called.
Rivals Australia and South Africa will square off in the second Test of the ongoing four-match series at St George's Park, Port Elizabeth, starting on Friday.
In comments likely to strain already frosty relations between the teams, Warner put the blame for the incident squarely on De Kock's shoulders.
"I think everybody just needs to focus on cricket". Rabada went on to pick up tow more wickets to finish at 21-2-96-5.
They picked off the runs after that measured start, with Warner accelerating by hitting nine fours.