All Blacks, Springboks maintain 100pc records
Pair set for showdown but Kiwis will be without injured Richie McCaw for rest of the tournament
In New Zealand, flyhalf Dan Carter became the first man to reach 1,400 test points to help his side to a 28-13 win over Argentina in Hamilton, though the victory was tempered by a serious knee injury to skipper Richie McCaw.
For South Africa, prop Coenie Oosthuizen put the visitors in front after six minutes and their advantage was extended with late tries from captain Jean de Villiers, Zane Kirchner and Willie Le Roux.
The win in front of 43,715 spectators at Lang Park was the Springboks' first victory at the venue in eight attempts.
"I thought our defence was awesome," Springbok coach Heyneke Meyer said.
"I truly believe we won the game firstly in our minds and secondly without the ball because the whole message was we needed to make more than 150 tackles.
"If they get momentum they are a very good side. I was very happy the way we attacked at the end. We really believed we could win. We wanted to show if you work together nothing is impossible."
The win puts South Africa on top of the Rugby Championship with three wins ahead of a meeting with New Zealand, who are also unbeaten, and Meyer cautioned his side to stay grounded ahead of next Saturday's clash at Eden Park.
"A lot of things worked, but we need to keep our feet on the ground and stay humble because next week is a bigger challenge," he said.
Wallabies coach Ewen McKenzie is still searching for his first win after three games.
"It doesn't matter who you play if you drop the ball in key moments and they counter-attack it's hard work," he said.
"There are bits of the game that are improving slowly but you are judged on the scoreboard and that's not an acceptable outcome. We made it too easy for them in the second half."
Meanwhile, McCaw, who had only recently returned to rugby after a six-month sabbatical, suffered what coach Steve Hansen thought was a torn medial ligament in his left knee after prop Charlie Faumuina had fallen on the flanker's leg in a tackle.
"It was a bit more serious. It looks like he's done a medial. How bad? It's not grade one, it will be a two, three or four," Hansen said when asked of the severity of McCaw's injury picked up in a match played at a rain-lashed Waikato Stadium.
Hansen said later that McCaw was likely to be out of action for up to five weeks, ensuring he will miss the remainder of the four-nation tournament.
The Pumas had opened the scoring but the All Blacks eventually seized control in a stop-start game.
"It was a messy win," number eight Kieran Read said. "We wanted to be positive but sometimes the conditions don't allow that. I think you have to be prepared for what gets thrown at you and in conditions like this and a physical Pumas side it probably took us a little bit longer to adapt."
Argentina are still searching for their first victory after opening the competition with home and away defeats against South Africa.
"Very tough conditions... very tough game," Argentina captain Juan Martin Fernandez Lobbe said. "We defended more than we attacked. We will look at the video and there are some tries we can avoid. I thought we had a chance. Now Australia next Saturday and we will get ready."