Eddie Jones' Brave Blossoms extended Wales' record losing streak to 18 games after winning the first of their two matches 24-19 on Saturday thanks to a furious second-half fightback.
First-half tries from Ben Thomas, Tom Rogers and a penalty try looked to have put Wales in control in hot and humid Kitakyushu until Japan scored twice in the second half to snatch the win.
"We lost out to them in the first half but our DNA is to play high-tempo rugby," said Japan flyhalf Seungsin Lee.
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