Green was struck in the groin by South African fast bowler Corbin Bosch by a high full toss just two balls before being dismissed in the 48th over of Australia's innings, going down in obvious pain when attempting to pull a bouncer to the boundary.
Green fell onto his back after the stroke and needed to compose himself before leaving the field of play, not to return to the rest of the match.
The 27-year-old was slated to bowl "a few overs" according to series captain Mitchell Marsh, having not yet bowled on tour as he manages his workload ahead of the three-Test series.
Green had bowled just ten overs in the two-Test series at home to Bangladesh in August, partly due to being surplus to requirements with Australia's full time quicks ripping through the tourists in Mackay.
His prognosis was not immediately clear after the match but it does leave him in doubt not only for the first Test but a two-day warm-up game against a South Africa XI in Potchefstroom this weekend, which would have served as crucial match practice for his red ball bowling.
Matt Renshaw was set to accompany Green in the first Test as Travis Head's opening batting partner, but he too is now questionable after being struck in the right wrist when fielding in close during South Africa's batting innings.
He left the field during the 14th over and did not return, with Australia forced to send out Marnus Labuschagne and Beau Webster as supplementary substitute fielders.
Australia won the match by 45 runs on DLS after South Africa's run chase was cut short by rain, handing the home nation a 2-1 series victory.
Marsh was uncertain about Green's condition in his post-match press conference.
"He had a nice buildup, and it would have been nice for him to have a bowl," Marsh said. "But it wasn't meant to be, and I'm sure that it won't affect his prep too much - hopefully."
Absences from Green and Renshaw would plunge Australia's batting order into chaos, with backup wicketkeeper Josh Inglis having already been sent home with a broken finger.
It even led to rumours - denied by Marsh himself yesterday - that the Aussie white ball captain could have been asked to stay in South Africa for a potential Test recall.
The Aussies could instead be forced to call upon someone from Australia A's tour of India, during which Victoria wicketkeeper made 128 batting at number seven against India A in Puducherry.
The tour also features capped batters Sam Konstas, Nathan McSweeney and Peter Handscomb.
