Khawaja, who has been out in the middle for every minute of this final Test match, strolled to the changeroom on 195 not out to bring an end to another gray day for the Proteas' bowling attack.
But before Khawaja reached his highest Test score, the SCG faithful was treated to a history-making knock from Steve Smith.
South Arica did well to control the opening 40 minutes as Smith and Khawaja consolidated their overnight position. But once the initial onslaught from the relentless Anrich Nortje and Kagiso Rabada was over, runs flowed.
Spin twins Keshav Maharaj and Simon Harmer - who currently combine for figures of 217/1 in 56 overs - failed to provide the control needed to create pressure. Smith and Khawaja took a particular liking to Maharaj, whose economy rate of 4.3 left much to be desired.
Khawaja brought up his hundred before lunch with Smith well-set on 59, taking the hosts to 266/2 at the break.
Smith moved along nicely after lunch and would raise his bat for a memorable century. His 30th Test ton moved him past the legendary Donald Bradman, but perhaps even more remarkable is that it was only Smith's second against South Africa, against whom he averages 40, some 20 runs less than his sparkling career average.
Somewhat anti-climatically, Smith chipped one back to Maharaj on 104, handing the spinner his first wicket of the series, though it was met without celebration. That brought Travis Head to the crease and with the hosts at 356/3, the left-hander showed his intent early on.
Under an increasingly darkening sky, the wicketkeeper quickly moved to his half-century, showing disdain for even the best of deliveries. Head's bludgeoning 70 off 59 finally came to an end when he went after an accurate short ball from Rabada, only to find substitute fielder Rassie van der Dussen on the ropes. After making a great catch low to his left, van der Dussen spun around and gestured to a group of rowdy spectators, grinning from ear to ear.
It was a rare moment of joy for the Proteas attack, who - Nortje aside (2/55) - have looked lackluster under the guidance of Dean Elgar. The under-fire captain has arguably been too conservative in his approach since losing the toss, seemingly waiting for mistakes rather than forcing them.
Matt Renshaw finally emerged from his boundary banishment following a positive Covid-19 test, but would only face a handful of deliveries before rain brought the days play to an end with Khawaja five short of a maiden Test double hundred.