A fourth successive Test defeat was registered as the Springboks fought back from a 21-point deficit surrendered inside the first quarter to prevail 42-39 in a mesmerising opening instalment of the series.
It is England’s worst run since 2014 and the pressure is continuing to build after a stunning opening salvo of tries from Mike Brown, Elliot Daly and Owen Farrell was followed by a dramatic collapse partly induced by the recurring flaw of indiscipline.
Jones, who was verbally abused by South Africa fans in the tunnel after the match, believes the Springboks had ridden their luck as his team dropped to fifth in the global rankings.
“South Africa have used a get out of jail card and sometimes you don’t get that again,” said Jones.
“They know they were in one hell of a game, they got home and did well to get home and deserved the victory.
“They’ll take confidence from the result, but we’ll take confidence from this game as well. Not at all will it be hard to pick the players up.
“The way we played in the first 20 minutes is the way we want to play all the time. This game has set the series up fantastically well.”
While England return to Umhlanga on the Indian Ocean to begin preparations for Saturday’s second match at Free State Stadium, South Africa celebrates a landmark moment in the nation’s history.
As the Springboks’ first black Test captain in their 126-year history, the reign of Siya Kolisi got off to a scripted start and the meaning of the occasion is not lost on Jones.
“It’s a big moment for the country to have Kolisi as captain and for him to win his first game at Ellis Park, the spiritual homeland of the Springboks,” said Jones.
“It’s an enormously symbolic thing for South African rugby and shows that transformation is working. Kolisi will be a good captain, let’s just hope he’s not too good in this series.
“While I’m desperately unhappy to have lost the game, I think it’s a great thing for rugby generally and for the game here particularly.”
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 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 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 the hosts in disarray he sent Farrell over under the posts.
But S’busiso Nkosi’s charge to within inches of the whitewash was followed by the outstanding Faf De Klerk spinning over, stemming the flow of points at the other end 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 winger touched down.
The dream debut continued when he popped up on the opposite wing after a clever run from Willie 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 Handre Pollard, combined with Nkosi keeping his width, provided the platform for him to exploit a large hole in midfield.
Two penalties from Pollard opened up a five-point gap and it was worrying times for England.
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.
South Africa: le Roux, Nkosi, Am, de Allende, Dyantyi, Pollard, de Klerk, Vermeulen, du Preez, Kolisi, Mostert, Snyman, W. Louw, Mbonambi, Mtawarira. Replacements: van der Merwe, Kitshoff, T. du Toit, P. du Toit, Notshe, I. van Zyl, Jantjies, Gelant.
England: Daly, May, Slade, Farrell, Beaumont, Ford, Youngs, M. Vunipola, George, Sinckler, Itoje, Isiekwe, Robshaw, Curry, B. Vunipola. Replacements: Cowan-Dickie, Marler, Williams, Shields, Hill, Spencer, Francis, Solomona.