Belgium, who have climbed to fifth in FIFA's world ranking after an unbeaten qualifying campaign, were undone by a 44th-ranked Japanese team that exposed the hosts' defensive frailties.
Marc Wilmots's side, who will take their place in Brazil next year for their first World Cup finals in 12 years, lost 2-0 to Colombia last Thursday.
For Japan, due to make their fifth consecutive World Cup appearance, it was proof of further progress after they produced some effective one-touch football to come from two goals down and draw with the Netherlands on Saturday.
There was some mitigation for Belgium, however, as they were without captain Vincent Kompany and striker Christian Benteke.
They also started brightly, opening the scoring in the 15th minute. Kevin Mirallas had an easy tap-in after Romelu Lukaku raced on to a through-ball from Dries Mertens, rounded Japan keeper Eiji Kawashima, and slid the ball goalwards.
A Yoichiro Kakitani header made it 1-1 at halftime.
Japan took control in the second half, going 2-1 up with a rasping shot from an unmarked Keisuke Honda and adding a third when Yoichiro Kakitani neatly chipped over the Belgian defence to an advancing Shinji Okazaki.
Toby Alderweireld's header pulled one back for the hosts, and the crowd urged Belgium forward for a final push in the last 10 minutes. Kevin De Bruyne came closest to an equaliser, forcing a decent save from Kawashima in the final minute.
Belgium, whose loss to Colombia was their first defeat in a year and their first at home since September 2010, will be among the seeded teams in Brazil.
(Reporting by Philip Blenkinsop, editing by Stephen Wood)
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