Cheslin Kolbe and Makazole Mapimpi finished off England as South Africa’s impressive forwards powered them to a third World Cup crown.
Handre Pollard and Owen Farrell traded penalties in the first half, but the Boks had the edge thanks to their impressive scrum.
England were unfortunate to lose prop Kyle Sinckler to such an early injury, but they could have few complaints in Yokohama.
The Boks were dominant and Mapimpi got on the end of his own chip through to stretch the lead before Kolbe danced South Africa into the history books.
England have made habit of fast starts under Eddie Jones, but it was the Boks on the front foot from the off.
Pollard missed a penalty inside the first two minutes, but that was a range finder.
When Sinckler was forced off inside three minutes after accidentally colliding with Maro Itoje’s elbow, the Boks got on top of the scrum.
Billy Vunipola’s poor pass from a retreating scrum put Farrell under pressure and when man of the match Duane Vermeulen won the turnover we had an idea of things to come, Pollard putting them in front from the penalty.
The Boks were not just rolling up front, Damian de Allende and Willie le Roux were looking dangerous with ball in hand as well.
England levelled things up somewhat against the run of play when Farrell bisected the posts after Kolbe came in at the side.
The physical barrage was gruelling, in addition to Sinckler, the Boks lost Lood de Jager and Bongi Mbonambi in the first half.
But Tendai Mtwarira was having a field day at scrum time against Dan Cole, and Pollard was on target once again to restore the Bok lead.
Then came England’s best passage of the half, 25 phases of continuous pressure on South Africa’s line. Both Vunipolas went close but the Boks somehow held on, and England had to settle for a penalty that Farrell slotted.
The half-hour mark came and went and England were lucky to be level, but two more Pollard penalties, the first from another Vermeulen turnover and the second again at scrum time meant the Boks had a well-earned 12-6 lead at the break.
England came roaring out of the traps in the second half, with George Kruis on for Courtney Lawes in an attempt to shore up the scrum.
But the Boks were quick to introduce Steven Kitshoff and Vincent Koch with the same result, another penalty slotted by Pollard for a 15-6 lead.
England turned to Joe Marler, on for Vunipola, and after an initial issue, Jérôme Garcès penalised the Boks front row and England had a foothold.
Farrell drilled the three points, Henry Slade was on for George Ford and England had half an hour to trim a six-point deficit.
A Tom Curry turnover then breathed more life into the comeback attempt, but Farrell’s penalty drifted wide and Pollard went right up the end and pushed the lead back out to nine.
Farrell hit back immediately however, as the Boks got muddled from the restart and ran into each other.
Luke Cowan-Dickie and Mark Wilson were the next men introduced, while Pollard did not have the distance with a shot from his own half.
But the clock was ticking, and then the Boks administered the killer blow. Mapimpi chipped over the top, Lukhanyo Am collected and returned it to the winger to go over for a fantastic score.
Pollard drilled the extras, and at 25-12 with less than quarter of an hour to go, the game was all but up.
Youngs went quickly from a penalty and released Anthony Watson for a surge down the right but again the Boks held firm.
And then they finished things off in superb style off turnover ball, Slade knocked on and Kolbe pounced and jinked up the right wing for the icing on South Africa’s cake.
