Steve Clarke's side defended with a mixture of diligence and desperation in this 2020 European Championship qualifier only for all the good work to be undone just before half-time when a lapse of concentration ended with striker Romelu Lukaku heading in a cross from skipper Eden Hazard.
In truth, the goal had been coming and the Manchester United striker added a second in the 57th minute with a strike and Steve Clarke's side had to work hard to prevent further damage before Kevin De Bruyne added a third in the final minute.
Roberto Martinez's all-star team, ranked number one in the world, have won four out of four Group I fixtures while the Scots have six points from 12 and host Russia and Belgium in their next qualifying double-header in September, their task of qualifying for a major tournament for the first time since 1998 not becoming any easier.
The nerves that the 4,000 or so members of the Tartan Army had would have increased with the news of skipper Andy Robertson's absence through injury, his place taken by 21-year-old Kilmarnock left-back Greg Taylor.
Clarke made five changes from Saturday with striker Oliver Burke, who came off the bench to score the dramatic late winner against Cyprus, starting along with attacker Johnny Russell and midfielders Scott McTominay and Stuart Armstrong with Charlie Mulgrew wearing the armband.
The visitors had a clear-cut chance in the ninth minute when Burke found himself behind the Red Devils' defence from Armstrong's flick but he failed to connect properly with his angled-drive and the ball slipped past the far post.
Belgium surged back. Eden Hazard found De Bruyne with a clever pass but the Manchester City midfielder's drive was tipped over by keeper David Marshall, who then saved a long-distance effort from Axel Wetzel.
The pressure kept building. Taylor got caught at the edge of the box taking a pass from Russell and De Bruyne drove wide of the target before a better effort had Marshall stretching to tip the ball over the bar.
Armstrong was replaced by Ryan Fraser in the 32nd minute and it looked like the Scots would make it to the interval unscathed only for Lukaku to head in Hazard's cross from the byeline, when McTominay switched off for a moment.
The stunned Scots should have gone 2-0 down four minutes into the second-half when Lukaku headed a cross from Thomas Meunier over the bar while under no pressure.
Two minutes later Marshall beat away a terrific 25-yard free-kick from De Bruyne but after another ferocious drive from the Etihad stadium attacker had been parried by Marshall, Lukaku followed up past Taylor to return the ball into the net from 12 yards.
Lukaku drove narrowly past the far post as did Hazard when he worked himself into a shooting position. Yet another strike from Lukaku missed the target although with 10 minutes remaining Fraser drew a decent save from Thibaut Courtois with a curling shot.
The Belgium keeper then rushed from his goal to deny defender Scott McKenna before substitute James Forrest, on for Russell, failed to capitalise on the loose ball.
Marshall denied De Bruyne as the home side returned fire but he was eventually beaten beaten by the brilliant Belgian who drilled in from the edge of the box.