Head coach Jones toasted a new dawn as Manu Tuilagi, Freddie Steward and Raffi Quirke claimed stunning tries before Marcus Smith nailed a last-ditch winning penalty.
Handre Pollard slotted five penalties but missed two crucial shots at goal for the Boks, who mustered just one try from Makazole Mapimpi and further goals from Elton Jantjies and Frans Steyn.
England leaked 18 penalties and failed to dominate in the tight, but Harlequins maverick Smith’s masterful broken-field play eventually won out.
And with star youngsters like Smith, Steward and Quirke breaking through across a fruitful autumn, Jones admitted the quest for the 2023 World Cup title hurtles ever closer.
Asked if this autumn series represents a new England era, Jones replied: “Yes, we said in the summer that the Lions tour draws a line in the sand, and that you need to regenerate and have a little bit of a rebirth to go to the World Cup.
“There’s some good players coming through but we’ve got some pretty good experienced players too.
“They feel comfortable within themselves, they want to be together, they want to work together.
“Our stated aim is to win the World Cup, so we want to be better in the next campaign.”
Smith’s poise among the chaos of South Africa’s brutal defensive onslaught points to a playmaker quickly en route to the game’s very summit.
Jones insisted Smith still remains a “work in progress” however, despite the 22-year-old starring in the absence of injured regular captain Owen Farrell.
“Well he’s a work in progress, and each game he’s going to get a little bit better,” said Jones, of Smith.
“I thought he did a great job today, but he’s going to be better in the Six Nations.
“I know he will be because he’s got a great desire to keep learning and to keep on getting better.”
Asked if Smith will be England’s starting fly-half in future, Jones continued: “You can’t make those predictions as we’ve seen.
“We had a captain and a vice-captain that we don’t have any more because they are injured or out with Covid.
“Marcus, as long as he keeps improving, he’s going to have a good role in this team.”
South Africa smashed England 32-12 in the 2019 World Cup final, with Jones’ men falling short at the final hurdle in Japan.
England’s bid to lift the Webb Ellis Cup for a second time quickly switched to France in 2023, and Jones is excited by the energy of the latest new recruits.
“This series just gives the players a lot of confidence I think,” said Jones.
“With the first try against Australia and a couple of tries we scored today, we’ve added some really good, aggressive attack into our game.
“At times the Springboks got on top of us in the set-piece, but we managed to edge out enough quality possession to score enough points.”
Asked if this win represents payback for losing the 2019 World Cup final, Jones added: “No, I think as I said before the game, it’s a one-off game between the first and the third in the world.
“We’re happy to knock off the top team in the world.”
South Africa boss Jacques Nienaber lamented the Springboks’ third slender defeat of the calendar year, but insisted the reigning world champions are still moving in the right direction.
“It’s obviously disappointing, it’s the third Test this year that we’ve lost that way, having led late on,” said Nienaber.
“We don’t finish the game and that’s something we’ll have to look at and we’ll have to improve, but it’s very disappointing.
“This is a team that’s better than its win percentage. It’s a team that’s better than that.
“But in saying that I think we lost a lot of development in 2020 because we didn’t play any Test matches.
“So this year has been for us, and I’ve made no fuss in saying that I don’t think we’re there yet.
“But now we know what we’ve got to build on and there’s a lot we can work on.”