Goals from Steven Defour and Kevin Mirallas made sure of the three points at a rain-sodden Hampden Park and a point in Croatia next month will seal their spot in the tournament for the first time in 12 years.
Marc Wilmots' side broke the deadlock seven minutes before half-time sending the 7,000 visiting fans into pandemonium.
Toby Alderweireld's low cross was superbly turned home by the right-foot of Defour in one swift movement, giving goalkeeper David Marshall no chance.
It was the 25-year-old FC Porto man's first international goal in five years and he was only in the side due to an injury picked up by Eden Hazard.
They wrapped up the win with two minutes remaining when Christian Benteke's superb through ball was missed by Grant Hanley and that allowed Everton striker Kevin Mirallas to score his eighth international goal with a cool finish.
Belgium fired out an early warning when Kevin De Bruyne's corner was bundled just past the post from close range by Christian Benteke as the visitors exerted some early pressure.
There was another close call when Nacer Chadli whipped a tempting ball to the back post where Marouane Fellaini nodded just wide of the target, with the ball taking a slight deflection off Whittaker.
Scotland were dealt a blow when Robert Snodgrass picked up a booking after nine minutes for foul on Axel Witsel, ruling him out of next week's qualifier in Macedonia, before he was the victim of a challenge that earned Fellaini a caution moments later.
Belgium continued to press for the opener and Toby Alderweireld tried his luck with a strike from the edge of the area that Marshall claimed at the second attempt.
At the other end, Scotland had a great chance of their own when Mulgrew teed up the shot for Celtic team-mate Brown and the skipper unleashed a powerful effort that fizzed just past the post.
Marshall was called into action again on what had been a busy night for the Cardiff keeper so far when he did well to smother Witsel's volley.
But he could do nothing to prevent the breakthrough after 38 minutes when a heavy touch by Whittaker gifted Fellaini possession and he released De Bruyne down the right flank, who cut the ball back for Defour to rifle beyond the grasp of Marshall.
Belgium were keen to add to their goal after the restart and Chadli stung the palms of Marshall with a fierce shot, before Benteke drilled wide of the target.
The Scots were just as determined to haul themselves back into the match and Whittaker surged into the box only for the end product to let him down as his shot went past the post.
Hutton then went to ground under pressure from Chadli but there was no spot-kick award from Italian referee Paolo Tagliavento.
With the hour mark approaching, Snodgrass was withdrawn from the action and Ikechi Anya was handed his Scotland debut.
The Watford winger was quickly involved in the action when he burst down the left flank before picking out Maloney for an effort in front of goal he could not keep on target.
Griffiths was then swapped for Rhodes, before Nicolas Lombaerts hobbled out of the action and was replaced by Sebastien Pocognoli.
Scotland could have restored parity with 10 minutes to go when Brown squared into the path of the onrushing Rhodes, who stabbed past the post from six yards.
But there was no way back as the Red Devils doubled their lead with two minutes to go when Benteke's pass found substitute Mirallas and he shrugged off Hanley before lashing into the back of the net.