Aminiasi Tuimaba, Napolioni Bolaca and Vilimoni Botitu all found the tryline as Fiji flew into a seemingly unassailable 19-0 half-time lead in the Cup final.
South Africa scored 20 unanswered second half points to deny Fiji back to back titles at the Singapore Sevens.
The Blitzboks remain fourth on the overall standings after eight rounds, 24 points behind leaders USA.
England had earlier beaten Australia 31-19 in the quarter-finals, but lost their semi-final 26-12 to Fiji.
Fiji cracked under that pressure and gave away a penalty inside their own 22-metre line, which Selvyn Davids converted to give his side an impressive come from behind win.
Fiji won the restart and with time up Aminiasi Tuimaba attempted a kick and chase but the Blitzboks got to the ball first to clinch their second tournament victory of the season.
Meanwhile, newly crowned Singapore champion South Africa leads Pool A with Argentina, Canada, and Japan.
But, despite the desperate start and being without some of their key players, South Africa dug deep and pulled off an epic comeback in the final - one which will galvanise this young team heading into the final stages of the World Series and begin to build for the 2020 Olympics.
England is pooled with New Zealand, Scotland and the unnamed 16th team in Pool C, while U.S. leads Pool D with Australia, Wales, and Spain.
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