Japan started and finished strongly, scoring first and adding the last 17 points of the match. But in between Fiji produced a series of spectacular tries to build a 33-10 lead.
Two of those tries went to winger Joji Nasova, who scored just before and after halftime while lock Mesake Vocevoce crossed for one try and helped create another. Captain Tevita Ikanivere also scored in the period between the 23rd and 43rd minutes when Fiji took the game away from Japan.
Fiji were hard-pressed to hold on in the second half against a resurgent Japan team who scored tries through hooker Heyate Era — his second of the match — and fullback Ichigo Nakakuso to close the margin to six points.
Japan had Fiji under enormous pressure when they were reduced to 13 men in the second half with back-rower Viliame Mata and prop Eroni Mawa in the sin bin.
"We overcame a tough Japan team who came back in the second half because of the pace they brought and the ill-discipline we had," Ikanivere said.
"We talked all five weeks of this competition about plowing the field and coming to harvest today."
Fiji were crowned champions for the second year in a row and sixth time overall. The final was played in the United States for the first time, at America First Field near Salt Lake City.
Tonga beat Canada 35-24 in the playoff for third place.
"We're a bit disappointed," Japan captain Warner Dearns said.
"We probably let them get away from us a little bit in the first half and we couldn't bring it back in the second."
Earlier on Saturday, Samoa rallied from 28-5 down at halftime to draw 32-32 with Chile in the first leg of a two-leg Rugby World Cup qualifying series.
The loser still has a chance to qualify through a repechage tournament in Dubai in November involving Belgium, Namibia and either Paraguay or Brazil.
Chile qualified for the 2023 World Cup after beating the US by a point on aggregate in a two-leg qualifier.
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