The springboks are placed second on the table with 14 points tied with the All blacks who are ranked first just with one round of the Rugby Championship left.
Tries from scrum-half Jaden Hendrikse, centre Damian De Allende, a brace from hooker Malcolm Marx and a penalty try ensured that Boks won the match 36-20 and got a bonus point.
Argentina are on nine points while Australia have 10 points.
High Penalty count
Los Pumas paid for a high penalty count, numerous handling errors and poor discipline that saw half-backs Santiago Carreras and Gonzalo Bertranou sin-binned in the first half.
South Africa also had two players yellow carded, but a strong first 40 and a powerful finish proved enough.
The unflappable Emiliano Boffelli knocked over the first penalty of the game for Argentina on nine minutes but moments later Damian Willemse replied for the visitors.
Both kickers then missed their second efforts from close to the halfway line, but after that it was one-way traffic.
The first try came after 22 minutes as South Africa created space down the right for wing Canan Moodie.
Although Carreras stopped him with a try saving tackle, the Argentine fly-half then jumped up from an offside position to put in another crucial block to hold up Hendrikse over the line.
A second Boffelli penalty kept the Pumas in touch but the Springboks soon made the extra man count as Hendrikse sold a dummy before strolling in under the posts, Willemse kicking the extras.
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Argentina’s high penalty count was gifting South Africa good field position and ramping up the pressure on the 14 men. From a driving maul, Marx was powered over by his pack, although Willemse missed the extras.
Scrum-half Bertranou was yellow carded and Lood de Jager bulldozed over for what would have been a fourth South Africa try, only for Doleman to rule there was a knock-on in the build-up as the Boks led 22-6 at half-time.
Argentina came out fired up in the second half after but the tide appeared to be turning in their favor when Willie le Roux was sent to the bin after a string of South African infringements.
And so it proved as Argentina were awarded a penalty try when K Smith, who was also shown a yellow card, after he tackled Tomas Cubelli around the neck as he stretched for the line.\
Almost immediately, Matias Moroni made a stunning break though the heart of the Springbok defence to dot down under the posts and Boffelli’s conversion made it a two-point game, with South Africa still down to 14 men.
But De Allende powered through two tackles to score from close range and Marx benefitted from tired tackling to score in the corner as South Africa extinguished Argentine hopes.
The Wallabies are placed third with 10 points after victory was ripped from them, courtesy of one of the more dramatic refereeing interventions in the history of their fixture against All Blacks going down to 39-37.
Game week six fixtures
New Zealand vs Australia Sat, 24 Sept 10:05
South Africa vs Argentina Sat, 24 Sept 18:05