Kolisi, in his first match in seven weeks following a hamstring injury, trudged off in the 25th minute. He may be a doubt to lead the Springboks back home against New Zealand in two weeks in the opening Test of the blockbuster Greatest Rivalry series.
"I hurt my hamstring again unfortunately," he said. "It's tough but I can't be sad about it. There's nothing I can do but go in for a scan and see how long I'm out for."
- New Zealand begin South Africa tour with flattering win over Stormers
- Watch New Zealand's tour of South Africa live on Sky Sports
- Ben Earl slams 'brutal' Nations Championship schedule
- Not got Sky? Get Sky Sports or stream with no contract
The skipper was among a core group of Springbok stalwarts given match time in Buenos Aires after missing the Nations Championship in July because of injuries.
Caps record-holder Eben Etzebeth and fly-half Sacha Feinberg-Mngomezulu played every minute and lock Lood de Jager, coming back from a hip injury, lasted until the third quarter.
They got to celebrate a 12th straight Test win, but only just.
The depleted Pumas almost snatched a draw after the full-time whistle. From a tap penalty in front of the Springbok posts, they pounded the visitors for 15 phases until the final high pass to an unmarked Matías Moroni was dropped.
Argentina Coach Felipe Contepomi pounded the coaches' booth and Moroni was in tears.
Watch South Africa's four-Test series against New Zealand live on Sky Sports. Get Sky Sports or stream rugby with no contract.
