With their backline in tatters and trailing 10-0 early after a try to debutant Leroy Carter, the Springboks scored 36 unanswered points in an extraordinary onslaught a week after falling 24-17 to the hosts at Eden Park.
Cheslin Kolbe lit the spark with a try in each half, while Damian Willemse, Kwagga Smith, RG Snyman and Andre Esterhuizen also crossed for the Springboks.
The All Blacks' previous worst defeat was also against the Springboks, a 35-7 setback at Twickenham in the lead-up to the 2023 Rugby World Cup.
The result threw the Rugby Championship wide open and followed Argentina's 28-26 win over Australia in Sydney.
"We knew it was going to come," said inside centre Willemse.
"It was just a very good week from us. Credit to the boys, they stepped up and played a fantastic game of rugby."
It was a win made all the sweeter by the challenges thrown at the visitors, who lost lock Lood de Jager, flyhalf Sacha Feinberg-Mngomezulu and fullback Aphelele Fassi in the first half to injuries.
They trailed 10-7 at the break, with only Kolbe keeping them in the hunt with an intercept try.
But they regrouped brilliantly through their replacements and the strength of their forwards.
The Boks pack won a decisive scrum penalty three minutes from the restart, with captain Siya Kolisi making a midfield break to set up their second try.
Replacement centre Esterhuizen flung the ball wide to Kolbe who danced over at the right corner.
Three minutes later, Kolbe was wincing in the hands of trainers after a no-arms tackle by lock Tupou Vaa'i.
Manie Libbok knocked over the penalty to stretch the Springboks' lead to 17-10.
The All Blacks' resistance proved futile against a tidal wave of green jerseys as the Springboks ran riot at Wellington Regional Stadium.
Willemse crossed near the hour-mark, beating three defenders, before Smith joined the try-fest with his own in the 69th minute.
Snyman, earlier denied a try due to a knock-on, then barged over in the 73rd minute, with Esterhuizen completing the rout with the team's sixth try six minutes later.
Shell-shocked All Blacks coach Scott Robertson said his team had no excuses for their dramatic fade-out.
"We've got to be really, extremely honest with each other," Robertson said.
"We thought we had a really good week but obviously it wasn't deep enough preparation."Â
