Thomas Meunier opened the scoring for Belgium in the 4th minute with a close range finish from a Nacer Chadli's cross.
Eden Hazard sealed the game for Roberto Martinez's men when he fired past Jordan Pickford in the 82th minute.
Eric Dier went the closest for England in the 70th minute, but Toby Alderweireld made a brilliant goal-line clearance to deny him.
A much changed England line-up was ineffectual in the attack with only couple of good chances in the entire match.
The bronze-medal finish for Belgium is its best performance at the World Cup.
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