Nonu did not emerge for the second half at the Westpac Stadium in Wellington as the All Blacks claimed a 14-10 victory to go six points clear at the top of the table.
And the 32-year-old appears set to miss the remainder of the competition after the severity of his injury was revealed by coach Steve Hansen.
"We've got a pretty good idea of Ma'a's prognosis," Hansen said. "We think it's probably broken. He felt sore and the doctor decided he wasn't right at half-time."
South Africa also suffered a damaging injury blow, with scrum-half Ruan Pienaar ruled out for the rest of the tournament after sustaining damage to medial knee ligaments.
Despite the defeat, Springboks coach Heyneke Meyer expressed pride at his side's spirit.
"I will never be happy when the Boks lose, even if it's away from home against a great team like New Zealand," Meyer said.
"But I'm very proud of the way in which the guys played, especially our youngsters. The All Blacks probably used their opportunities better and they probably adapted better to the wet field.
"We wanted to keep the ball in hand, but made a number of mistakes close to their tryline. Credit though to the All Blacks, they are a quality side. We gave our best and in the end it wasn"t good enough.
Meanwhile, Hansen was similarly pleased with New Zealand's mental fortitude following a triumph that significantly boosts their hopes of winning the trophy for a third straight year.
"The character of the side has been tested a few times over the last couple of years and they keep coming up with an A-plus pass mark," Hansen added. "Once again they did that tonight.
"They put themselves under pressure at times, making poor decisions with our kicking. In doing so that allowed the Boks to attack us from unstable platforms and defensive platforms and yet we showed a lot of courage to keep them out. It is one thing we're very proud of."