In the morning, Elgar and Rabada frustrated the Australians for 50 minutes as they build South Africa's overnight total from 266 for 8.
Australia ended the day's play on 9/245 and trail by only 66 runs.
However, his attacking innings was cut short by pacer Kagiso Rabada. He sliced a no-ball for four, then was bowled by a ball which went between bat and pad with Warner stuck on his crease. Fellow opener Cameron Bancroft made a stoical 77.
It was then Nathan Lyon who played the role of saviour for the Aussies as he set a new career high by piling on 47 runs from 38 deliveries.
Rabada was also in the midst of it for the second wicket to fall, taking the catch at backward square leg that dismissed Usman Khawaja off Morkel.
David Warner has once again found himself in the middle of a controversy. Warner was clearly unimpressed with what the fan had to say and began to argue with the elderly gentleman.
However, one fan decided he had to pick up the slack as Warner made his way up the stairs. However, after security incharge's intervention, Warner headed back to the pavilion.
Warner was fined and docked three demerit points for the tirade he launched at Quinton de Kock during the first test at Kingsmead - also on the stairs leading to the dressingroom.
To the South African players' credit, no player exchanged in any verbal barbs as Warner trudged towards the dressing rooms.
Cape Town - David Warner has been involved in another staircase altercation. this time with a spectator at Newlands. Elgar, the nuggety South African opener, finished unbeaten on 141. Elgar batted for 434 minutes, faced 284 balls and hit 20 fours and a six. That helped keep Australia to 245-9 in their first innings, 66 runs behind South Africa's 311 in a test where the victor can't lose the series.
"We can't control that, unfortunately", South Africa bowler Morne Morkel said of fan behavior.
Although ten other fielders shared the record, Smith was only the second Australian to achieve the feat after Vic Richardson in 1935/36.
Warner's exchange was less violent but more prolonged, immediately after he had lost a gladiatorial bout with Rabada.
For reasons unknown, Khawaja didn't seem interested in sticking around at the crease and he played a weird shot off the bowling of Morne Morkel.
Warner has scored 185 runs in the series so far at an average of 37 with two half-centuries to his name. That total includes his 75 during the second innings of the Test in Durban.
Vizcarra set to become Peru's new leader
Vizcarra is expected to hold the post of president until July 2021, when Kuczynski's term was due to end. They appeared likely to accept his resignation letter overnight, rather than having an impeachment trial.