England won the final 21-14 but beaten opponents South Africa gained the most from the Tokyo leg of the world sevens series.
The Blitzboks recorded a fourth successive runners-up finish on Sunday but, importantly for them, they finished ahead of arch rivals Fiji and New Zealand to open up their lead atop the standings with two tournaments to play.
South Africa are on 129 points going into the eighth and ninth legs in Glasgow and London in May while Fiji, who they pipped 7-5 in the semi-finals, are on 125.
New Zealand remain rooted in third on 120 after suffering a shock 19-15 loss to 11th-ranked Canada in the quarter-finals.
Australia are among the biggest losers of the round as they are now nine points behind fourth-placed England in the race for the automatic Rio 2016 Olympic Games qualification places.
The All Blacks Sevens suffered their first loss in 29 matches against the Canadians after both teams scored three tries but New Zealand missed all of their conversion attempts.
They bounced back in the Plate competition to beat France 19-12 and then Scotland 21-14 to finish fifth, earning some valuable extra points.
They face a stiff task to win a fifth successive series crown, having won just one event out of seven this season – their home tournament in Wellington in February.
England, whose loss in the final in Wellington had been their best previous result of the series, were deserved winners of a tense final.
It was locked 7-7 at halftime but England broke the game open through tries captain Tom Mitchell and Phil Burgess before veteran playmaker Cecil Afrika gave his team late hope with a try.
England move ahead of Australia into fourth place in the series.
The top four finishing teams qualify automatically for the Rio 2016 Olympics, where sevens will make its Games debut.
South Africa 129pts, Fiji 125, New Zealand 120, England 100, Australia 91, United States 71, Scotland 67, Argentina 66.