Steve Borthwick's men led by nine points in the final quarter but their wet-weather masterclass began to fade as the 'Bomb Squad' made their presence felt for the Springboks, especially in the scrum.
It was on the back of their set-piece ascendancy and the generalship of replacement fly-half Handre Pollard that the tables turned in a sodden Paris.
RG Snyman barged over for the only try of the match in the 70th minute and Pollard nailed a tricky conversion, setting up heartstopping finish to a Test that was enthralling throughout.
The world champions were still two points behind but up stepped man-of-the-match Pollard to land the killer blow with two minutes left, nailing a penalty from just inside England's half.
England's players sank to their knees at the final whistle, their hearts broken having given their all in a rematch of the 2019 final despite being distant outsiders, and it was an especially cruel moment for Owen Farrell given his outstanding night.
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