Januzaj’s superb second-half goal sent Belgium into a last 16 clash with Japan while England will now advance to a second round meeting with Colombia on Tuesday.
By finishing second in the group, England have though avoided a loaded top half of the draw containing past winners Brazil, France, Argentina and Uruguay as well as European champions Portugal.
The fact second place in the group was no disaster seemed to be a big factor in both coaches’ team selection with their places in the last 16 already secured.
Southgate made eight changes with Belgian boss Roberto Martinez going one better as only Thibaut Courtois and Dedryck Boyata retained their places from the 5-2 thrashing of Tunisia.
Star Belgian duo Eden Hazard and Kevin de Bruyne joined England captain Harry Kane in watching from the sidelines and their ability to thrill was badly missed as locals in the crowd turned on both sides with jeers and chants of “Russia”.
Youri Tielemans did test Jordan Pickford with a fiercely struck effort just six minutes in that forced the Everton stopper into his best save of the World Cup so far.
Moments later Pickford let a Michy Batshuayi effort squeeze past him and was rescued by Gary Cahill’s goal-line clearance.
After an early burst, though, Belgium seemed more adept at picking up yellow cards that would have seen them finish behind England if the game ended in a draw due to a poorer disciplinary record.
Tielemans and Leander Dendoncker both went into the book early to cheers from the Belgian fans.
Six of England’s eight goals against Tunisia and Panama to reach the knockout stages came from set-pieces and they again proved the Three Lions greatest threat in the first-half as Cahill and Ruben Loftus-Cheek headed just wide.
Marcus Rashford had the opportunity to put serious pressure on Raheem Sterling for his place in the side for the last 16 after two disappointing performances from the Manchester City winger.
But unlike his substitute appearance against Tunisia, Rashford failed to further his case for a start and fired well off target when presented with a shooting chance from the edge of the box just after half-time.
Januzaj suddenly sparked the game into life moments later when he twisted and turned inside the England box before curling a wonderful strike into the top corner.
Rashford had by a distance England’s best chance 25 minutes from time, but again slotted wide with just Courtois to beat.
Belgium were given a major boost ahead of the knockout stages when captain Vincent Kompany made his return from injury for the final 15 minutes.
Southgate didn’t even turn to Kane in search for an equaliser, instead introducing Danny Welbeck to ensure every outfield player in his squad featured across the three group games.
And Welbeck nearly earned a point eight minutes from time when his goalbound effort was deflected just wide by Fellaini.
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