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The Springboks used their power in the early stages of the game and Marcell Coetzee was able to go over the tryline in the 13th minute following a breakdown of a maul from a line-out on the Australian five-yard line.
The visitors hit back with a penalty as Bernard Foley fired his kick between the posts, and it got better for the Wallabies when they took the lead on an incisive breakaway as Ashley Cooper touched down in the corner.
South Africa managed to regain their composure in the second half and they drew within two points of the Aussies as they won a penalty from a ruck, which Handre Pollard lifted over from close range.
The Springboks pressured Australia throughout the second half but couldn't find a way through the solid backline until Pat Lambie showed great touch and accuracy to put a drop-goal through the posts and give his side the lead.
The floodgates soon opened as the home side dominated the final seven minutes of the match. Jan Serfontein broke with speed upfield and released Cornal Hendricks, who in turn found Jannie du Plessis. The second row offloaded to his skipper Jean De Villiers, who went over for the score.
Australia tried to rally and got the ball back into the South Africa half, only to be hit on the break again. This time Lambie went himself and faked the offload before powering over the line.
The Springboks ended the game in style when De Villiers scored his second try of the match with a surging run to the corner, while Lambie added the conversion.