AB de Villiers made a patient, unbeaten half-century as South Africa closed on 238 for five in their second innings at Newlands, extending their advantage to 294 runs on a wicket that has significant sideways movement.
South Africa's crushing win gave them a 2-1 lead in the four-match series, with Australia facing an internal inquiry into the ball tampering scandal and having only four days to regroup before the final Test starts in Johannesburg on Friday.
Cummins said it was "up there" with his best spells in test cricket.
"I think it's been disgraceful", Lehmann said.
"From the beginning of the series with all of the stuff that has gone on, I've kept saying we need strong officials in a series like this with two tough teams going after each other", he added.
Elgar and Rabada frustrated the Australians for 50 minutes as they took South Africa's overnight total from 266 for eight.
The batsman got into a verbal slanging match with Quinton de Kock after the South African used what the batsman called "vile and disgusting" about his wife Candice.
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"It's not on at a cricket ground anywhere around the world, not just here".
"There have been various incidents throughout the Test series but this one has taken the cake".
Lehmann, when asked about an incident of racial abuse levelled at Hashim Amla in Hobart during 2016, made it clear that was "not good enough from an Australian crowd point of view".
Cummins didn't let that happen with his brilliant burst.
Four balls later, the spinner repeated the dismissal as Morkel (4) was also gobbled up by Smith, a fifth catch of the innings for the Australian to equal the most ever in test history, one of 11 outfield players to achieve the feat. He was the top run-scorer in test cricket in 2017.
Cameron Bancroft was the man tasked with executing the plan, but cameras caught him in the act and it resulted in an emotional post-day confession from the 25-year-old opener and his captain. Du Plessis, Bavuma, and de Kock all followed quickly, trapped on their crease by Cummins and edging behind to the slips or wicketkeeper Tim Paine.
"Ball shining versus ball tampering are two very different situations and one is much more serious than the other. I look at the awesome achievement over four days, the way we applied pressure to the Australian team in all facets of the game", said Du Plessis.
Former South Africa skipper Graeme Smith, commentating on television, said he was aghast that the ball had not been changed immediately when the tampering pictures were shown on television, adding that the umpires had been remiss.