The win puts Belgium into the quarterfinals, setting up a mouth-watering clash with Brazil in the last-eight.
Genki Haraguchi broke the deadlock for Japan three minutes into the second stanza with a low strike from the right side of the box following a quick counter-attack.
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Roberto Martinez's side beat Japan 3-2 after it looked like they were out of the competition when they were losing 2-0 at 52 minutes. As the Red Devils compete for the World Cup in Russian Federation, the Spaniard brought in from England two years ago is getting credit for moulding a "golden generation" of talented individuals into a multicultural, multilingual team that he says can turn Belgium's awkward divisions into a strength on the field. Vertonghen made amends for making the error that gifted Japan its opening goal.
Jan Vertongen started Belgium's comeback in the 69th minute before Marouane Fellaini came off the bench to make it 2-2 five minutes later.
Belgium's winning goal came on a counterattack launched in injury time. Romelu Lukaku dummied Meunier's cross, leaving Nacer Chadli wide open at the back post to win it for his country.