Gareth Southgate's side needed at least a draw to ensure their chances of topping Group A2 remained alive going into their final game against Iceland.
However, first-half goals from Dries Mertens and Youri Tielemans put the hosts on track for a win that leaves them needing just a point in their final group game against Denmark to reach the Finals.
Belgium made a strong start to proceedings as some front-footed defending from Jan Vertonghen was followed by the ball being fired up toward Tielemans, whose shot took a deflection off Tyrone Mings before going in off the post just 10 minutes in.
England almost hit back immediately, Harry Kane's header from a corner being brilliantly cleared off the line by Romelu Lukaku.
But Roberto Martinez's men doubled their lead shortly after, Mertens curling in a fine free-kick despite the visitors' protests that Declan Rice had not committed a foul in the build-up.
With Southgate's words clearly ringing in their ears, England started the second half on top, winning a succession of free-kicks at the edge of the Belgium box before Kane forced a save from Thibaut Courtois with a low drive.
The visitors could not make the most of their chances, however, a theme that continued following the introduction of Jadon Sancho and Dominic Calvert-Lewin from the bench and ensured their evening would end in defeat.