Johnson continued his remarkable start to the three-Test series, snatching a wicket in each of his first two overs after Michael Clarke set the hosts a target of 482 early on day four at Centurion.
Clarke ended Australia’s innings at 4(dec)-290 after 3.2 overs on Saturday, and Johnson took five deliveries to have Alviro Petersen out edging for one.
In a repeat of the first innings, Johnson required two balls to remove Smith.
In the first dig a fearsome bouncer directed at the skull of the Proteas captain brought about his downfall; this time debutant Alex Doolan’s catch was responsible.
Smith forcibly clipped a full ball from Johnson off his pads, only for it to land straight in the hands of short leg Doolan who was stationed deeper than usual.
Hashim Amla (22 not out) saw off the rest of Johnson’s opening spell, wearing a rearing ball in the grill, and did well to reach the meal break.
Peter Siddle trapped Faf du Plessis (18) lbw with a skidding delivery in the fourth last over of the session, removing the right-hander that caused Australia so much trouble in the famous draw at Adelaide Oval in 2012.
Amla and AB de Villiers (4 not out) will need to do incredibly well if South Africa are to survive five sessions on a wearing pitch where cracks are causing havoc.
Especially in light of the 150km/h pace and dangerous bounce created by Johnson’s slinging action.
Johnson is in the form of his life and has looked even more potent in this match than in the recent Ashes series, where he claimed 37 scalps.
The left-armer’s haul of 7-68 on Friday set a new mark for his best Test figures outside Australia.
He currently has 2-27 in the second dig and three more wickets would make for Johnson’s greatest match figures.
No Test side has ever scored more than 418 in a successful fourth-innings run-chase.
But the Proteas have form when it comes to salvaging draws.
“If you look back on Adelaide when we put 500 runs on the board, it was a tough battle,” David Warner said after scoring a century on Friday, referencing the way the Proteas batted for four and a half sessions in 2012.
“It’ll be a tough battle here.”
With no Shane Watson to ease the quicks’ workload, Warner (0-3) sent down two overs of medium pace on Saturday.