South Africa are 6-140, trailing Australia by 257 runs, but it could have been much worse after a brutal opening spell from Johnson saw the left-armer take three wickets.
Day two began with Shaun Marsh and Steve Smith continuing after their successful rescue mission on day one. They didn’t last long however, with Smith falling soon after making his 100, followed by Brad Haddin for a duck and then Marsh for 148.
Johnson put some of the batsmen to shame compiling his 33 runs, with Ryan Harris putting on 19 of his own as the tail wagged to just short of 400 to be all bowled out for 397.
The South Africa innings began with a bang, Graeme Smith took Harris for 10 runs off his first over but then copped a beauty from Johnson in the second which he could only sky to Marsh in the cordon.
Alviro Petersen didn’t last much longer dangling his bat at a wide one from Johnson that he just nicked to Haddin’s gloves to leave the Proteas reeling at 2-15.
Faf du Plessis, who brought the Aussies plenty of trouble last time they visited Australia, showed little resistance but could hardly be blamed after another short rocket from Johnson ballooned to Clarke.
The meant Hashim Amla and AB De Villiers, the top two ranked batsmen in the world, were at the crease to bring some order to their innings.
Amla seemed able to handle Johnson, but was brought undone on 17 by a clever in-swinger from Peter Siddle, given not out by the umpire but plumb on review.
Nathan Lyon chipped in with the wicket of JP Duminy, another South African who’s performed well against Australia, caught by Johnson trying to go over the top.
Johnson’s wasn’t finished either. He bowled Ryan McClaren who played all around a straight one.
The only chance for the big score remains De Villiers, who is unbeaten on 52 but nursing a nasty knock on the elbow.
Play will begin three minutes early tomorrow to make up for lost time today.
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