Sayers sent Rabada packing two balls later, but Bavuma and wicketkeeper Quinton de Kock ensured South Africa didn't lose anymore wickets as they put together an unbeaten 14-run stand before stumps was called.
New Australia captain Tim Paine had complained after the opening day that his side were "flat" at times and they appeared so again, the usual intensity in their performance visibly lacking.
And after the South African's brilliant 152-run knock on Friday, Kohli praised the batsman with emojis.
Former Australian cricket vice captain David Warner has apologised for his role in the ball-tampering crisis that saw him suspended from the sport for 12 months.
Faced with the mammoth South Africa's first innings score of 488, Australia made a complete mess of it as they dished out a cricketing equivalent of stage performers fluffing their lines and then running back stage embarrassed to leave behind a perplexed audience. Khawaja and the Marsh brothers all fell in the space of five overs.
Playing in his final Test Morne Morkel came to the crease to massive acclaim but he was out first ball edging a nasty lifter from Cummins, with a diving Peter Handscomb taking an excellent catch at second slip.
Australia look the second new ball through an extra half-hour to the close, and Sayers got his first Test wicket when De Villiers edged behind, which was upheld on review. Batting on 27 off 80 balls, Amla wafted at a leaden-footed drive off Pat Cummins, in the middle of Australia's best spell of the day.
The Australian fightback was launched by Pat Cummins (3/53) who has been consistently their best bowler and their leading wicket-taker when he dismissed Markram and Du Plessis with successive balls.
Sayers, Handscomb and Renshaw all took catches.
Earlier in the day, Nathan Lyon had an appeal that was unsuccessful against ab de Villiers; replays showing the ball was set to miss leg-stump. But he stonewalled questions about who was aware of the plot and whether it was the first such incident within the team.
"In striving to do so I have made the decision which has had the opposite effect and it's one that I will regret for as long as I live".
Coach Darren Lehmann, convinced to step down after seeing the apologies from Bancroft and Smith, was also tearful as he announced his resignation.
The usually pugnacious batsman, 31, repeatedly struggled to talk and tears ran down his face as he apologised to fans, team-mates, his family and the Australian public.
Bancroft was caught on camera trying to use sandpaper to alter the ball, an offence which triggered an outpouring of criticism from home and overseas against the hard-nosed Australian team.
IOS 11.3 Released, Introduces New Tool To Stop Performance Throttling
Thanks to Health Records , information regarding immunizations, medications, procedures, allergies, and more will be stored in one location.