According to Radio Sport, Taylor suffered a torn calf muscle rather than just a strain.
A recovery for that injury tends to vary from two to six weeks, which would rule Taylor out of the tests in Wellington and Hamilton.
"He was looking a bit stiff," teammate Trent Boult said after earning the team's best figures of four for 64 earier in the day. "He looked disappointed. The way he walked off didn't look too good."
Taylor was hitting form for the Black Caps following surgery on his left eye to remove a pterygium in December. He scored two half centuries in the test series against Bangladesh before scoring ODI centuries against Australia and South Africa to become the nation's record holder for most ODI tons.
South Africa is one of two test nations, along with Bangladesh, Taylor hasn't scored a test century against. Whether he'll get another chance to face the Proteas in the long form of the game is doubtful.
New Zealand toured South Africa last year and probably won't play them before the 2019 Cricket World Cup, a tournament Taylor has mentioned as a possible swansong to his successful career.
Colin Munro and Neil Broom loom as contenders to replace Taylor based on middle order Plunket Shield form.
Meanwhile, Martin Guptill will undergo a six week-long strength and conditioning rehabilitation programme before returning to cricket.
Guptill has suffered hamstring strains to both legs across the summer. Following medical consultation, he will miss the remainder of the New Zealand domestic season and the beginning of the Indian Premier League.
Black Caps physiotherapist Tommy Simsek said: "At the moment Martin isn't fit to play and the time we give him now to strengthen his hamstrings will play a big role in mitigating future risk.
"We've put a programme in place to make sure that Martin can return to full strength and we'll continue to monitor him closely."
New Zealand coach Mike Hesson said: "Having Martin fully fit is critical, as we all know the positive influence he has on our side.
"Martin knows this is an important period to get back to 100 percent so that he can be fully confident when he is on the park.
"The Champions Trophy isn't far away."
Guptill will travel to India ahead of the start of the IPL where he will continue to be monitored by Simsek.