Fast bowler Kagiso Rabada faces a hearing on Sunday that could result in a ban from the third Test against Australia.
Rabada, who devastated the Australian batting order on the first day, has been charged following an incident with Australian captain Steve Smith on Friday.
After winning a leg before decision against the Australian captain, Rabada shouted in celebration and approached Smith aggressively. Their shoulders made contact.
South Africa were 153 for two at tea in reply to Australia's first innings of 243, with Elgar and Amla unbeaten on 57 and 54 respectively.
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Only 43 runs were scored in 26 overs between lunch and tea after a slightly less pedestrian morning during which 71 runs were scored in 28 overs.
Opening batsman Elgar, renowned for his gritty defensive qualities, was even slower than usual, taking 164 balls to reach his fifty. By tea he had faced 191 deliveries.
Amla, normally more fluent, took 122 balls to reach fifty and by tea had faced 144 balls.
Amla was twice given out leg before wicket, on seven against Pat Cummins and on 40 against Josh Hazlewood, but surivived on review on both occasions.
Australia bowled accurately and their fast bowlers gained reverse swing, which troubled both batsmen.
The only wicket to fall was that of nightwatchman Rabada, who was bowled by Cummins for 29 in the ninth over of the day.
The most dramatic incident of the afternoon followed a request by the umpires for a brass band, which provides a regular backdrop to cricket at the ground, to be quiet.
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