Hong Kong can still join them despite the loss at the National Olympic Stadium after they finished second in the standings, providing they come through the four-team repechage.
They will face Uruguay in the semis and, if they win that, either Russia or an African team in the final for the last place in Pool A alongside the hosts, Wales, Australia and either Fiji or the Cook Islands.
However, they will need to sure up a porous defence if they are to have any chance of a first World Cup appearance with Japan's swift back play and powerful scrum and maul resulting in easy points in a lopsided win.
The four-try bonus point was bagged before halftime with impressive winger Yoshikazu Fujita grabbing two as the Brave Blossoms went in 27-3 up at the break.
Fujita completed his hat-trick in the second half of the eight try rout, the final game at the stadium before it is torn down to be replaced for a new facility for the 2019 World Cup which they will host.
South Korea beat Philippines 55-22 on Saturday to ensure third place in the championship, with Sri Lanka last after four defeats.
Japan have won all 28 matches in the Asian Five Nations since its inception in 2008 but coach Eddie Jones, previously in charge of Australia, will be aiming to lead the 'Brave Blossoms' to a first win at a World Cup since 1991.
(Writing by Patrick Johnston, editing by Pritha Sarkar)
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