The counter-attacking tail-ender was given a taste of his own medicine - reverse swing - and edged behind cheaply as Rabada finished with 11 wickets in the match. Rabada has four in just his 28th Test.
Rabada was charged with a level two offence after he made contact with the Australian captain after taking his wicket on the opening day of the second Test.
South Africa clinched the series leveling win on Monday by chasing down the meager target of 101 before tea on the fourth day.
Rabada's shocking discipline has dismayed West Indian great Holding who has served as somewhat of a mentor to the 22-year-old tearaway being compared to Malcolm Marshall.
Rabada also explained how his passion and emotions sometimes get the better of him after he takes a wicket.
Pat Cummins fell to a sharp catch at gully by Theunis de Bruyn and Mitchell Starc edged a drive to wicketkeeper Quinton de Kock. Dean Elgar was caught and bowled by Lyon off a leading edge for 5, in a near carbon-copy of his dismissal in the first innings in Durban, and Markram was caught at second slip by Smith off Hazlewood for 21, but all that did was bring de Villiers to the crease.
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That took his total of points after three previous offences to eight and triggered an automatic two-Test ban.
Before the verdict was announced, a remorseful Rabada said: "It's going to have to stop".
"The charge against KG is a level 2 with three demerit points, and the charge against Davey is a level two with three demerit points", said du Plessis.
Jeff Crowe of the Emirates Elite Panel of ICC Match Referees said: "I found that there was contact between Rabada and Smith, and in my judgement the contact by Rabada was inappropriate, and deliberate".
Proteas' players celebrate after Kagiso Rabada took the wicket of Australia's Mitchell Starch. Overall, however, Australia remain ever so slightly more likely to close out the win - they are 3/1 to claim a 2-1 series scoreline, and 11/4 for 3-1, compared to 5/1 and 8/1 for South Africa to secure the opposite result.
If an appeal is lodged‚ the team management said‚ Rabada "will still be suspended unless the judicial commissioner is appointed early and hears an argument to allow him to still compete whilst the hearing is being sorted out".
For his part, Rabada said he would need to avoid getting into close proximity with opponents. I don't think we've got any indiscretions as far as I know.
The express paceman was found guilty of inappropriate and deliberate physical contact with Steve Smith in Port Elizabeth, having brushed the batsman's shoulder in a send-off.