Johnson went from intimidatory to outright unplayable in a fiery opening spell on Thursday, snaring 3-5 and making Proteas captain Graeme Smith look like a tailender.
Earlier, it took almost five hours for centurions Shaun Marsh and Steve Smith to grab the advantage with a record 233-run partnership, lifting Australia to a total of 397 and a lead of 257 when rain caused an early stumps.
Johnson needed only 3.1 overs to make it a vice-like grip.
It would be unfair to suggest the left-armer continued his form of the Ashes, where he claimed 37 English scalps to be man of the series.
This was more destructive.
On a bouncy Centurion pitch where his slinging action had the ball travelling over 150km/h, Johnson was at his brutal best.
He finished with figures of 4-51 and landed a painful blow on the forearm of AB de Villiers (52 not out), who offered the most resistance.
First in the firing line was Smith, who looked comfortable taking 10 runs from the opening over bowled by Ryan Harris.
Smith, whose hand Johnson has broken twice, was ungainly in his belated attempt to take evasive action in the second over and a menacing ball directed at his skull hit the bat handle.
Alviro Petersen's self-inflicted dismissal was next, the opener's attempted cut gifting wicketkeeper Brad Haddin a regulation edge.
Faf du Plessis, unsure if he should come forward or rock back to a ball on a perfect length, jutted his bat tentatively and the edge flew to Michael Clarke at second slip.
De Villiers counter-attacked, hoiking Johnson for a six when the 32-year-old returned for his second spell.
He batted impressively, but will need a partnership of substance with Robin Peterson (10 not out) to give the Proteas hope in this match.
Johnson later returned to shatter the stumps of Ryan McLaren, while Peter Siddle captured the prized wicket of Hashim Amla lbw for 17 when Clarke successfully reviewed Aleem Dar's decision.
JP Duminy shared a 67-run stand with de Villiers, but his attempt to put Nathan Lyon out of the park ended with Johnson running back from mid-off to snaffle a fantastic catch.
Earlier, Dale Steyn (4-78) cleaned up the tail as Australia lost 6-66 when a 400-plus total loomed.
Smith and Marsh bettered Ashwell Prince and Herschelle Gibbs' 213-run effort against Pakistan in 2007, setting a new mark for the best fifth-wicket Test stand at the venue.