His performance could well prove to be a match-winning one, as the 34-year-old helped South Africa recover from 183/6 to post 382 all out - a first-innings lead of 139 - before Australia were reduced to 180/5 in reply, just 41 runs ahead.
The ICC announced on Monday morning that Rabada, who rattled through the Australian batting line-up and now has six wickets in their second innings, will have to answer a Level 1 offence for his send-off of controversial opener David Warner on Sunday.
Rabada took two more wickets, including a crucial late breakthrough to get Usman Khawaja out for 75 seven minutes before the end of the day.
"It's a relief at the moment it happens and then it starts to sink in a few hours afterwards, sometimes only days afterwards", he said. 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 went to his 22nd Test century before lunch with a characteristically innovative stroke, arching his back and helping a short ball over the slips and to the boundary.
Rabada had earlier dismissed David Warner (13) - although he risks further sanction after a send-off that saw him scream in the batsman's face - and Shaun Marsh (1), while fellow seamer Lungi Ngidi removed Cameron Bancroft, the opener bowled for 24 via an unfortunate deflection off his left boot.
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.
Rabada's hearing over a level-two charge for making physical contact with Australia skipper Smith unfolded behind closed doors after play on day three of the second Test.
"Well it'll be handy for us not to have to face him, that's for sure", said Australia assistant coach David Saker. "South Africa are very blessed to have him in their team".
Rabada was the chief destroyer in the Australia first innings with 5-96, including a burst of 5-13 off 18 balls.
It was a near-identical replay to the spray he gave Smith, but on this occasion he didn't brush the batsman's shoulder.
Crowe read the riot act to both du Plessis and Smith between the first and second Tests, urging the rival captains to improve their teammates' behaviour and play the game in better spirits.
"It felt like 10 out of 10 to get my hundred, it was right up there with one of my best, and I was very nervous in the 90s". He returned to tests late previous year. I don't think it showed but I was telling Vern (Philander) out there 'I'm struggling to breathe here.' My legs literally went numb. "But I told myself that it wasn't about myself, it was about doing it for the team, and that helped, although it was still very hard after not scoring a hundred for three years", De Villiers said.