Springbok head coach Heyneke Meyer promised action against replacement prop Dean Greyling after he was yellow carded in the loss to the All Blacks.
Immediately after the match, won by the All Blacks 21-11, Meyer apologised to All Blacks skipper Richie McCaw, who appeared to be on the receiving end of a forearm smash by Greyling.
It was South Africa's second indiscretion in as many games.
Lock Eben Etzebeth was banned for two weeks for a headbutt in the Test against Australia and now Greyling faces the judiciary after he dived at McCaw, who was trapped in a ruck, and appeared to hit him in the face.
The incident came in the 63rd minute, just after the All Blacks had taken a 15-8 lead and were starting to take the ascendancy in a physical, torrid, match between two of rugby's most passionate rivals.
"I'm very big on discipline and it's unacceptable," said Meyer, who before the match had expressed his admiration for McCaw as "one of the best players ever".
"I think it cost us the game as well and I want to apologise to Richie and it will be dealt with inhouse, but it's unacceptable.
"We're a team that prides ourselves on discipline and we can't afford these things in games."
Visiting skipper Jean de Villiers said if Greyling is found guilty he will face internal action as well as any punishment handed down by the rugby judiciary.
"We'll never condone playing dirty," De Villiers said.
"Like the coach said, discipline is a non-negotiable for us and definitely if he was in the wrong we'll take action internally against him."
All Blacks coach Steve Hansen said the hit on McCaw was a "cheap shot" but would not comment further.
"It's not in our hands," he said.
"The referee and touch judge have yellow-carded it and the citing commissioner will have a look at it and make the decision but I thought it was a cheap shot and what happens next will be up to those people."
McCaw, three times the IRB's world player of the year and a veteran of 110 Tests, was not injured by the blow and brushed it off as "just one of those things".
The All Blacks have now won all four of their Rugby Championship matches to stay at the top of the table, while South Africa slipped to third behind Australia, who beat Argentina.
Against the fired-up Springboks, the All Blacks struggled in the first half and led 5-3 at half-time after South Africa's ace goal-kicker Morne Steyn was woefully off form and missed five of six shots at goal.
But the emergence of Aaron Smith after the break gave the All Blacks backs a quicker service and they began to break down the South African defence.
Smith, the first-choice scrum-half before being demoted to the bench for breaking team rules before the Test, further stamped his mark by scoring the game-turning try when the score was locked at 8-8 in the 60th minute.
He broke around the side of a ruck and raced 30 metres to score.
"I had a point to prove, and I was very happy when I got over the try-line," he said.