The former Manchester United and Sunderland man produced the game's only real moment of quality, working the ball onto his left boot and sending it past Jordan Pickford for the decisive moment.
England would have finished at the summit had they held on for a draw, but they now face a last-16 tie against Colombia, whereas opponents Belgium take on Group H runners-up Japan.
However, the Red Devils are on course to face Brazil in the quarter-finals, while the Three Lions will have a more favourable last-eight tie against Switzerland or Sweden if they make it that far.
Just short of 10 minutes of England's third group game had passed when Pickford made his first save of the tournament, doing just about enough to keep out a stinging shot from Youri Tielemans.
A bizarre moment shortly after saw Michy Batshuayi flick the ball goalwards for Pickford to collect, only for it to squirm out of his grasp to give Batshuayi a second attempt.
The prodded shot found its way past Pickford but was stopped before it could cross the line by covering defender Gary Cahill, who was one of seven England players to make their first start of the tournament.
All the best first-half moments were falling Belgium's way, as Marouane Fellaini controlled a corner with his chest and blasted the ball goalwards, where Trent Alexander-Arnold was waiting to block it before it could reach the back of the net.
England looked disjointed when attempting to put attacking moves together, with Marcus Rashford and Jamie Vardy barely getting a sniff in attack, and their only real opportunity culminated in Ruben Loftus-Cheek heading a corner into the ground and wide of the target.
The Three Lions were given an injury scare ahead of their first knockout-round tie with the enforced substitution of John Stones, and they were given a further setback on the field as they were behind with six minutes of the second half played.
One of the numerous Belgium players with Premier League experience to their name found the breakthrough goal - Januzaj rolling his boot over the ball to take Danny Rose out of the game, before bending one out of Pickford's reach.
Rashford squandered a glorious chance to level with an hour played, being denied by the fingertips of Thibaut Courtois - one of only two survivors for much-changed Belgium from their last outing - when played clean through on goal.
Not until the final quarter of the match did the two managers start turning to their bench, with Vincent Kompany given a first run-out in a month after sustaining an injury in the build-up to the competition.
Rashford dipped a free kick over the crossbar and Fellaini's block flew past the upright as England chased an equaliser, but it was Belgium who came closest to a second as Pickford parried a long-range drive from substitute Dries Mertens late on.
The evening would ultimately end in frustration for Gareth Southgate, who will feel justified in making eight changes to his starting lineup, as his side's 12-match unbeaten run came to an end in Kaliningrad.
ENGLAND (3-5-2): Pickford; Cahill, Jones, Stones (Maguire 46'); Alexander-Arnold (Welbeck 79'), Delph, Dier, Loftus-Cheek, Rose; Vardy, Rashford
BELGIUM (3-4-3): Courtois; Boyata, Dendoncker, Vermaelen (Kompany 79'); Chadli, Dembele, Fellaini, T. Hazard; Tielemans, Batshuayi, Januzaj (Mertens 86')