Playing his first match in seven weeks after a hamstring injury, Kolisi trudged off in the 25th minute on Saturday (Sunday AEST).
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," Kolisi said after the match.
"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."
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 flyhalf 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 hooter. 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 Matias Moroni was dropped.
Coach Felipe Contepomi pounded the coaches' booth and Moroni was in tears.
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