Ricky Januarie's brilliant solo try four minutes from time set up replacement centre Francois Steyn for the match winning conversion and he hit the mark to give the world champions a huge Tri Nations boost.
"You have to take your hat off to the Springboks. Their experience told and they came away with a very good win," said Fitzpatrick.
It was the Boks' first win in New Zealand for 10 years and their first triumph at Carisbrook since the south island venue hosted the first game between the two countries back on 13 August, 1921.
While it was victory at the eighth time of asking for Victor Matfield's men in Dunedin, it was defeat for the first time in five years on home soil for the All Blacks as their magnificent 30 match unbeaten run came to an end.
The Boks had to win the game the hard way because Matfield was given a yellow card for a high tackle, leaving his side a man short for the final 10 minutes.
It was a stunning reposte from the South Africans following their opening 19-8 Tri Nations defeat in Wellington the previous weekend. They now move on to Australia to meet the Wallabies in Perth next weekend.