Phil Burgess, Charlie Hayter and Tom Mitchell scored the tries in the final for the English, who bounced back from a thumping group stage defeat to Fiji on Saturday to win a first title since the Wellington Sevens in Feb. 2013.
"I am unbelievably proud of this team. It's a huge effort and we are so grateful to deliver this title," skipper Mitchell said after victory at a wet Prince Chichibu Memorial Rugby Ground.
The 22 points moved them onto 100 and ahead of Australia into the fourth and final Olympic qualifying position available from the series. Further spots are available for next year's Rio de Janeiro Games via regional qualifiers
South Africa still lead the way after collecting 19 for the runners-up spot to move onto 129, four clear of Fiji with only two rounds left in the series in Glasgow and London next month.
The Fijians, winners of the last two tournaments in Las Vegas and Hong Kong, picked up 17 points in Tokyo after edging Canada 21-19 to finish third.
The Fijian's hat-trick bid was ended by the South Africans in a nervy, error-strewn semi-final that the Blitzbokke took 7-5.
New Zealand, winners of 12 of the 15 Sevens World Series titles and reigning World Cup sevens champions, endured a disappointing week in the Japanese capital, suffering a first ever loss to Canada in the quarter-finals.
The 19-15 defeat sent them into the second tier Plate tournament, which they won after beating France in the last four and then Scotland in the final after Dylan Collier's try in the last play of the game. The 13 points keeping them third on 120.
Trans-Tasman rivals Australia dropped to fifth after a weekend to forget in Tokyo.
After losing to Portugal and Scotland in group play on Saturday, they then suffered a heartbreaking defeat to the United States in the lung-busting final of the third tier Bowl event.
Perry Baker scoring the match ending try in extra time as the ever-improving Americans prevailed 17-12.
Portugal won the Shield after edging Argentina 12-7 but last-placed Japan closed the gap on the Iberians to eight points in the battle to avoid relegation after picking up 10 for making a first Cup quarter-final.
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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