Khawaja and Mitch Marsh fought back fastidiously during an 87-run stand in Port Elizabeth on Sunday (Monday morning NZ Time), building a small lead as Australia reached 5-180 in their second innings. Bowling around the wicket he trapped Khawaja in front of his stumps with a full delivery after the left-hander made 75 off 136 balls.
Nightwatchman Kagiso Rabada was the only wicket to fall in the opening 54.3 overs of the day, with Elgar and Amla digging in as the tourists started to reverse-swing the old ball. Only Shane Bond has a better Test strike-rate in the last 100 years of Test cricket, and Rabada already has 45 more wickets than the New Zealander managed in his entire career.
De Villiers, who had not scored a ton in his last 13 tests, featured in an 84-run partnership with Vernon Philander for the eighth wicket as the pair saw off any potential impact of the new ball from an Australian attack that looked exhausted after their exertions on Saturday. "So you know you have to get to him quickly and it's important that some of our players get around KG before he gets close to the batsman", De Villiers said on Sunday. That incident on its own has the potential to see Rabada banned for two tests and miss the rest of the Australia series.
Khawaja had not enjoyed a happy series with the bat, extending a record overseas that does not almost stack up with his numbers in Australia.
He was the anchor in late partnerships of 44 with Quinton de Kock, 84 with Vernon Philander (36) and 58 off just 43 balls with Maharaj (30) to keep South Africa going.
This comes as he still awaits the outcome of his hearing on Sunday night for a Level 2 offence after he "brushed" the shoulder of Australian captain Steve Smith on Friday.
Match referee Jeff Crowe is expected to throw the book at South Africa spearhead Kagiso Rabada, who has disobeyed umpires' advice and unleashed yet another screaming send-off in the second Test.
No wonder David Warner and Nathan Lyon celebrated so exuberantly when they left him stranded without scoring in the second innings at Kingsmead.
Rabada had earlier courted more trouble ahead of a hearing on Sunday night (Monday morning AEDT) that was set to nearly certainly confirm his suspension for the rest of the series.
Saker said Australia had not lost hope.
While South Africa's best young bowler was both good and bad, its best batsman was sublime. There was a lot of emotion from that last Test match (in Durban) going into this one and once again as a fast bowler you want to prove things to people, and you want to show everyone you belong on this stage. I was quite nervous, I haven't been in this position for a while and it means the world to me.
"I just have a lot of sympathy. he's crossed the line a couple of times and I think he's regretting that". I told Vern I was struggling to breathe and my legs went numb.