And following the defeat, Australian Jones had an altercation with some South Africa fans in the tunnel after the final whistle at Ellis Park.
A fourth successive Test loss was recorded 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.
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.
New South Africa captain Siya Kolisi is tackled by Jonny May of England.
De Klerk, electric all season for the Sharks, helped set up S'busiso Nkosi for two tries before Le Roux crashed over minutes before the break.
The second-half was dominated by the Springboks whose customary physicality was matched by a cutting edged 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.
Jones, who was verbally abused by South Africa fans in the tunnel after the match, believes the Springboks had ridden their luck. They got home and did well to get home and deserved the victory. We started the game well. Not at all will it be hard to pick the players up.
With a fifth-place finish in the Six Nations to shake out of their systems, England were at it from the first minute as Wasps' Daly landed a mammoth penalty from inside his own half.
It was the flawless 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.
Kolisi's life journey from poverty and adversity in the township of Zwide in Port Elizabeth to becoming a rugby superstar and iconic figure in the history of South African sport will be inspiration enough for his teammates. Kolisi is hoping to reflect on his historic achievement after the three-match series against England has been won.
England at least emerged from a pulsating Johannesburg opener without any significant injury concerns, with Tom Curry and Daly suffering minor cramp and a dead leg respectively.
The dream debut continued when he popped up on the opposite wing after a clever run from Le Roux, creating the space for fellow debutant Aphiwe Dyantyi to send him over.
"Faf was excellent", Jones said.
But England suddenly lost momentum as South Africa found their straps with De Klerk dictating the pace of play in a triumphant return to his former home ground.
"That might have been the cause of some uncharacteristic individual discipline errors which allowed South Africa back into the game and they were able to piggy-back off 17 penalties to establish a lead".