A scarcely-believable 24-3 lead had been amassed by the 18th minute, with George Ford acting as ringmaster as Mike Brown, Elliot Daly and Owen Farrell ran in superb tries.
But the match was turned on its head when Faf de Klerk orchestrated a stunning first-half comeback supported by the brilliance of Willie le Roux that enabled South Africa to take a 29-27 lead into half-time.
Electric debutant S’busiso Nkosi crossed twice to bring Ellis Park to his feet and in between his two tries, Eddie Jones hauled off Nick Isiekwe - the Saracens lock who was making his full debut - and brought on the uncapped Brad Shields.
The second half was dominated by the Springboks whose customary physicality was matched by a cutting edge in attack overseen by De Klerk and Le Roux, but it was the boot of Handre Pollard that did most of the scoreboard damage through three penalties.
It was the perfect outcome to celebrate a landmark moment in South African history after back row Siya Kolisi had become the first black captain of their Test team.
England could barely have made a better start as a monster 61-metre penalty by Daly was followed by a try that started from inside their own 22.
Quick hands released Jonny May down the right wing with Ben Youngs in hot pursuit and several phases later, Brown was given sight of the line and he showed strength to shrug off two tackles and crash over.
South Africa came back hard but having been kept at bay, England struck again with Ford conjuring a superb try.
Henry Slade supplied an outrageous pass to Brown but the move was all about Ford as he picked out May and with the overlap appearing it was a simple run-in for Daly.
Two minutes later and they were over again, Slade’s long pass giving May space and with shell-shocked South Africa in disarray he sent Farrell over under the posts.
But Nkosi’s charge to within inches of the whitewash was followed by the outstanding De Klerk spinning over, stemming the flow of English points and initiating a high-octane fightback.
On the half-hour mark it was game on when a Springbok attack down the right was revived through their tenacity before De Klerk’s vision offered the lightning-fast Nkosi a half-chance.
The danger should have been averted but Daly made a mess of gathering Nkosi’s grubber and the alert Sharks wing touched down.
The dream debut continued when he popped up on the opposite wing after a clever run from Le Roux created the space for fellow debutant Aphiwe Dyantyi to send him over.
Le Roux then turned scorer from a scrum after De Klerk and Pollard, combined with Nkosi keeping his width, provided the platform for him to exploit a large hole in midfield.
Two penalties from Pollard - the second won at a dominant scrum - opened up a five-point gap and it was worrying times for England, who were barely able to get their hands on the ball.
When they did counter through Tom Curry a knock-on ended the attack and their frustration was clear when Mako Vunipola followed through on De Klerk, earning a yellow card.
And in the next play South Africa had all but sealed the outcome when Dyantyi juggled the ball while crossing the line before touching down.
Maro Itoje and May plundered late tries, but Pollard’s boot mean the Springboks had done enough despite a nervy finish.