The Springboks' 24-18 victory proved a much tighter contest than last week's meeting when they beat the Pumas 46-13 to win the Rugby Championship.
Kolisi, the Boks' first black test captain and a key figure for the side on and off the pitch, missed the entire global season with a knee injury but was able to prove his fitness with a solid display against the physical South Americans.
Argentina thought they had taken the lead with four minutes remaining, but the try was ruled out by the television official for an obstruction in the build-up. Argentina made 10 changes after being humiliated at home.
Springboks flanker Marcell Coetzee was off on 17 minutes and could not return after failing a head injury assessment test.
But there was plenty of mileage left in the contest, with Diaz Bonilla and Jantjies exchanging penalties before Pablo Matera pounced for a try from a line-out by the Boks line.
Scrumhalves Faf de Klerk, Herschel Jantjies and Cobus Reinach, wing Sbu Nkosi, the scorer of two outstanding tries against Argentina, locks Eben Etzebeth, Franco Mostert, RG Snyman and Lood de Jager, and hookers Malcolm Marx, Bongi Mbonambi and Schalk Brits, who captained his country for the first time on Saturday, will all be in the World Cup squad. Diaz Bonilla succeeded with a more hard penalty kick than that of Jantjies.
"The team we put together had a lot of different combinations, which is why it was a stop-start game."It finally arrived on 32 minutes when slick handling allowed Nkosi to step inside one opponent before holding off two others to score.
Nevertheless, the visitors went into the break with an 8-10 scoreline with a try from Guido Petti Pagadizaval at the stroke of half-time that was improved by Diaz Bonilla.
The Springboks moved ahead thanks to Nkosi's second try in the 48th minute, converted by Jantjies, before Argentina levelled at 18-18 as Matera crossed.