Taylor turned a delivery from Morne Morkel into the leg side and set off for a single late this afternoon, but was quickly reduced to a limp with a calf injury and needed assistance leaving the University Oval field moments later.
He has retired hurt on eight and it was unclear whether he would play any further part in the first test of the series.
New Zealand were well-placed at 148 for two but Taylor's departure, and a superb catch to remove Henry Nicholls for 12, left the Black Caps in a more vulnerable spot at 177 for three at stumps, but effectively four down.
But he has had his share of luck, with three edges falling short of the slips, and only a desperate lunge prevented him being run out on 72.
Jeet Raval played nicely for his 52, but opener Tom Latham had an early exit on 10.
South Africa's innings wrapped up shortly after the lunch on 308, with spinner Jeetan Patel and strike bowler Trent Boult capturing the final two wickets.
Opener Dean Elgar top-scored for the Proteas with a patient innings of 140.
New Zealand had taken four wickets in the first session, with Elgar finally falling to Neil Wagner, while Temba Bavuma was dimissed for 64 after the pair had combined for a 104-run partnership.
Patel came on to bowl specifically to remove the threat Quinton de Kock presented and got his man for 10.
