Johnson set a new mark for his best Test cricket figures outside Australia, finishing with 7-68 on Friday as the Proteas were rolled for 206 shortly before lunch.
Batting with the freedom created by a 191-run first-innings lead, Warner's response made the bouncy Centurion pitch look like a road as he cracked his sixth Test ton off 118 balls.
Alex Doolan, who fell 11 runs short of a century on debut, proved the perfect foil in a 206-run stand as Australia breezed to a total of 3-288 at the end of play.
Unbeaten batsmen Shaun Marsh (44no) and Michael Clarke (17no) scored freely ahead of the captain's declaration some time Saturday.
Already the hosts need to set a new fourth-innings run-chase Test record to snatch an unthinkable victory.
In two sessions Australia scored 270 runs.
Dale Steyn removed Chris Rogers with his first delivery but from then on it was incredible dominance of bat over ball.
Unsurprisingly Warner was the forefront.
The left-hander flayed the pacemen with ease, including three boundaries in one Steyn over.
But in a free-wheeling innings of 115, Warner was indebted to some sloppy fielding.
Vernon Philander missed a run-out chance when the aggressive opener was on 106 but, far more costly, were dropped catches on 26, 27 and 51.
None was easy but, frustratingly for Graeme Smith, the first was the most simple.
Substitute fielder Dean Elgar ran in from the deep and was well position to snaffle the ball, but it somehow slipped through his hands.
Alviro Petersen and Smith were responsible for the other two lives, both slippers leapt high and got to the ball but couldn't reel it in.
In scenes reminiscent of the past summer, everything seemed to go Australia's way.
Apart from the Proteas' floundering in the field, which included too many gifted runs, the Decision Review System (DRS) was a tale of two teams.
Smith challenged the umpire's verdict after two confident Morne Morkel lbw appeals, when Warner was on 97 and Doolan 54.
The margin was slender but he was knocked back both times - in sharp contrast to Clarke who had DRS to thank for the dismissals of Hashim Amla and Philander.