Silencing Absa Stadium's 52,000-strong crowd with a storming finish, the All Blacks beat the Springboks 26-21 after trailing by nine with 15 minutes remaining.
With fresh replacements helping lift the tempo in the final quarter, and the Boks tiring on a big recent match workload, two quick converted tries to battered captain Richie McCaw and wing Joe Rokocoko sealed it.
The All Blacks had only won one of their past four tests in South Africa stretching back to 2004.
"We played pretty well in the last 20 minutes which is the sign of a lot of pride and backbone," said coach Graham Henry, describing it as their most physical test for "a long time".
"I think also the conditioning window helped us. We put a lot of work in physically and I think it came through with their fitness in the end. "
Henry, with the New Zealand Rugby Union's (NZRU) blessing, controversially removed his top 22 players from the first half of Super 14 to keep them fresh for the World Cup starting in September.
The Springboks meanwhile were playing their fifth consecutive test, after most of them appeared in the Super 14 playoffs, and were backing up from a bruising victory over the Wallabies.
"The last 20 minutes it looked like a team that had been playing for seven weeks in succession," Boks coach Jake White said.
"When their reserves came on you could see the complete difference in the way they lifted the ante."
White admitted his previously unbeaten team let themselves down on home turf and would find it tough to now break the All Blacks' stranglehold on the Tri-Nations.
He hinted last week he would rest players from the return match in Christchurch on July 14 to freshen them up, with reports today suggesting up to 20 frontliners could be left at home.
It wasn't pretty, but Henry's All Blacks again showed they could rise to the big occasion as they aim to end a 20-year World Cup drought this year.
"We realised we had to hang in there and the chances would come. If we could up the tempo they might run out of legs and that's where we got our opportunities," McCaw said.
"Everything in the game the guys held the belief and showed their character. They didn't let anything faze them, even that intercept try when it would have been easy to drop their heads."
In an often fiery encounter with plenty of off-the-ball incidents to keep referee Alain Rolland guessing, the Springboks were awesome in the opening quarter.
At the 65-minute mark they led 21-12 after tries either side of halftime to standout flanker Schalk Burger, and Butch James, who snatched a stray Aaron Mauger pass to dash 35m.
But the All Blacks' scrum began to dominate, they sped the game up with quick lineouts and counter attacks. The loose forward trio McCaw, Rodney So'oialo and Jerry Collins bashed the ball up at will and halfback Byron Kelleher had a busy game, hassling the Boks into errors.
So'oialo sparked McCaw's try with a stunning kick return while replacement Leon MacDonald set up Rokocoko with the Springboks defence down to a walk.
The All Blacks now have another tough turnaround with the resurgent Wallabies looming in Melbourne on Saturday night.
The All Blacks don't arrive until Monday night as they rest sore bodies on the long flight across the Indian Ocean.
McCaw said the sluggish opening 20 minutes was the main area of concern.
"The key is to get it going from the start because some days you don't get out of jail. It'll be great to be able to start the way we finished. "