Youri Tielemans gained the first yellow card for Belgium, following a foul against Danny Rose in which the England player was tripped.
Belgium were hit with a second yellow card when Rose was again fouled but this time by defender Leander Dendoncker.
The first yellow card was awarded just 19 minutes in to the match, with Belgium already behind England in terms of yellow cards.
Breaking the 0-0 tie after halftime, Adnan Januzaj scored in the 51st minute, which was his first goal for Belgium in nine appearances for his country.
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England keeper Jordan Pickford leapt toward the top right corner and his fingertips grazed the ball, however, Januzaj’s kick reached the back of the net with ease.
England had several near misses, with Danny Welbeck and Marcus Rashford missing Belgium’s goal by inches.
The top team of Group G now faces the team which finished second in Group H and vice versa.
Given England lost and finished second in Group G, they will now face Columbia in their first match of the World Cup last 16.
England lost against Belgium tonight with a goal in the 51st minute (Image: GETTY)
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Winners of Group G Belgium will now face Japan on July 2 at the Rostov Arena.
England’s next game will be at7pmBST on July 3 at the Spartak Stadium in Moscow.
Live coverage of England's next match will be shown on ITV.
Englandhavenever lost an international match to Columbia, meaning their progression through the World Cup may not be too difficult.
So far Columbia have won two and lost one of their matches, losing 2-1 to Japan and beating Poland and Senegal to qualify for the last 16.
The first match of the final 16 will take place between France and Argentina on June 30 at1pmBST.