Rabada was found guilty of a level two International Cricket Council (ICC) code of conduct offence of "inappropriate and deliberate physical contact with a player" after leaning with his shoulder into Australia captain Steve Smith when he dismissed him in the first innings, an ICC statement said.
The 22-year-old Rabada, who took 11 wickets to help South Africa level the series 1-1, was fined 50 percent of his match fee and given three demerit points, which took him past the tally of eight that triggers an automatic suspension.
Cricket South Africa said it was seeking legal counsel about a possible appeal that could potentially make Rabada available for the next test in Cape Town, which starts on March 22.
"I found that there was contact between Rabada and Smith, and in my judgement the contact by Rabada was inappropriate, and deliberate," match referee Jeff Crowe said in an ICC news release.
"He had the opportunity to avoid the contact and I could not see any evidence to support the argument that the contact was accidental.
"It is also disappointing that this has happened the day after the pre-match meeting I had with both teams, where the importance of respect for opponents was highlighted."
Rabada also accepted a second level one charge of "using language, actions or gestures which could provoke an aggressive reaction from a batsman upon his dismissal" in his send-off to David Warner after dismissing the Australian opener on Sunday.
Rabada received a further 15 percent deduction of his match fee and an additional demerit point.
In an increasingly acrimonious series during which Warner, Australia spinner Nathan Lyon and South Africa wicketkeeper Quinton de Kock have also been punished by the ICC, Mitchell Marsh was added to that list on Monday.
The Australia all-rounder was fined 20% of his match fee and handed one demerit point for a level one offence of "using language or gesture that is obscene, offensive or insulting".
He was caught on camera swearing at Rabada after being dismissed early on the fourth morning.
Rabada missed the second test against England last year having reached four demerit points.
South Africa level series
South Africa made heavy work of reaching their modest target, before captain Faf du Plessis (2) and Theunis de Bruyn (11) guided them to 102 for four.
The 22-year-old Rabada was the outstanding performer on Monday as he ripped through Australia, who started on 180-5 with a 41-run lead.
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.
"Australia were never going to give in easily so you had to go to the reserve tank and give of your best," Rabada said after being named man-of-the-match.
The tourists lost Mitchell Marsh (45) in the first over as Rabada uprooted his middle stump before Pat Cummins (5) was well caught in the gully by De Bruyn.
Rabada got his third in quick succession as Mitchell Starc (1) edged a drive to wicketkeeper Quinton de Kock.
Lungi Ngidi (2-24) had Nathan Lyon (5) caught by De Kock, before Tim Paine (28 not out) and Josh Hazlewood (17) added 28 for the final wicket as Australia were dismissed for 239.
South Africa lost wickets regularly with opener Dean Elgar (5) going cheaply to be followed after lunch by Aiden Markram (21), Hashim Amla (27) and AB de Villiers for 28.
"We were outplayed in all aspects," Smith said.
Australia won the first test in Durban by 118 runs. The final two matches in the series will be played in Cape Town and Johannesburg.
