Rabada already had five demerit points on his record, and the three-point penalty for the offence means he incurs an automatic two-match ban.
Another three demerit points for his Level 2 offence could see him suspended for two Tests, effectively ruling him out for the remainder of the series.
"It's going have to stop. I'm also letting myself down". However they scrambled home for the loss of four wickets.
Rabada was also slapped with a lesser level one charge on Monday for his exuberant celebrations when he dismissed David Warner in the second innings.
Mitch Marsh is bowled by Rabada who now has four 10-wicket hauls in his 28 Test career
Match referee Jeff Crowe said: "I found that there was contact between Rabada and Smith, and in my judgement the contact by Rabada was inappropriate, and deliberate".
Rabada said he would need to avoid getting into close proximity with opponents. "I just asked the same question", he added.
"I think we're going on the sensitive side with everything at the moment". I was just exhausted of playing.
He was suspended on disciplinary grounds past year, when he reached four demerit points during South Africa's tour of England.
"With the Stokes incident I didn't contest it because I knew I did it", he said.
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One thing that isn't anticipated is a fizzling of the intrigue. "I would have loved to be playing in the next game, especially coming off a performance like that". Eight demerit points triggers a suspension of two Tests or four limited-overs games. And not repeat the same mistake. "I am not happy about it but time moves on", he told reporters on Monday.
Faf du Plessis has questioned global cricket's disciplinary approach, stunned that David Warner's staircase rampage and Kagiso Rabada's rowdy send-off could both be worth three demerit points.
He completed figures of 6-54 and a match aggregate of 11-150, the fourth time he has taken 10 or more wickets in a test.
Rabada, recently ranked the No. 1 bowler in test cricket, has also previously been disciplined three times for his actions after dismissing batsmen and served a one-test ban in England past year.
Warner, Quinton de Kock and Nathan Lyon were all charged after an acrimonious first Test in Durban, which Australia won by 118 runs. He tried one too many big shots and was caught in the deep by Ngidi off left-arm spinner Keshav Maharaj.
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Australia's task looked beyond it when Lyon also fell cheaply, for five, but Tim Paine (28 not out) and Hazlewood (17) at least pushed the tourists' advantage beyond 100.
Dean Elgar and Amla made half-centuries on the second day to contribute to South Africa's total.
Khawaja almost saw out the day, while Mitchell Marsh also fought bravely to make 39 not out while still recovering from a stomach bug he had on the first day of the game.
In the vastly complicated environment of South Africa where politics and sport are inextricably intertwined, there is a young man who in many ways represents the best of the post-isolation transformation of sport in our country.
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