After winning a leg before decision against the Australian captain, Rabada shouted in celebration and approached Smith aggressively.
Off-spinner Nathan Lyon said at the day one post-match press conference Australia would need to bowl well collectively on Saturday if they were to protect their sub-par first innings total of 243.
At the same time, he does not believe the Australian team will want Warner to tame his instincts too much.
Warner was fined 75 percent of his match fee for his involvement in a heated exchange with South Africa wicketkeeper Quinton de Kock as the two sides walked off the pitch on the fourth day in Durban.
"On behalf of CSA, I extend my honest apologies to the board of Cricket Australia (CA), its officials, team management, players and their families", CSA president Chris Nenzani said in a statement.
The Australian seamers made effective use of reverse swing for most of the second and third sessions to pose some hard questions for the batsmen, before Steve Smith took the second new ball just over five overs from the close.
Although held back by four different team mates during his verbal attack on De Kock, Warner said he did not intend to get physical with him.
The 21-year-old was picked ahead of the more experienced Morne Morkel in a surprise selection by the South Africans.
The feedback to the famous Port Elizabeth band wasn't all bad, though, with a handful of fans going against the grain and dubbing it the "best thing in world cricket".
South Africa have claimed the moral victory after the stairwell saga which culminated in Quinton de Kock being found guilty of a Level 1 offence, fined 25% of his Durban match fee and earning one demerit point after a hearing on Wednesday evening.
"I don't think so".
South African bowler Kagiso Rabada, second right, celebrates with teammate after dismissing Australia's Shaun Marsh, for 24 runs on the first day of the second test at St George's Park in Port Elizabeth, South Africa, Friday, March 9.
Coach Darren Lehmann and captain Steve Smith have offered public support for Warner, whose image has taken a hit just one month after he led Australia to Twenty20 tri-series success.
New footage shows the pair walking from the ground together and Warner is heard to call De Kock a "fucking sook", according to The Australian newspaper, referring to someone who is soft or easily upset. Rabada went on to pick up tow more wickets to finish at 21-2-96-5.
South Africa made an important breakthrough when Warner was bowled by Ngidi to follow Khawaja back to the dressing rooms after lunch.
He had Smith and Shaun Marsh out lbw, with both failing with reviews, and Mitchell Marsh was caught behind by de Kock attempting an expansive drive at an inopportune moment just before the tea break.