Steven Defour and Kevin Mirallas were on hand to guide the visitors to the victory in the pouring rain in Glasgow, earning just their second win on Scottish soil in six fixtures.
And with Scotland unable to qualify for Brazil next year, their visitors continue to top Group A, five points clear of Croatia with just two games left to play.
The match saw a number of changes for Gordon Strachan's men, who had David Marshall in goal following Allan McGregor's suspension, and Leigh Griffiths up front.
The 23-year-old filled the void left by Kenny Miller, who retired following Scotland's marginal 3-2 defeat to England at Wembley, after netting 18 goals over a 12-year international career.
For Belgium, however, things were generally more positive with three of their four injury doubts able to make the starting XI, with Eden Hazard gracing the bench.
And it was just over a minute before they threatened, with Chelsea midfielder Kevin De Bruyne's cross headed away by Russell Martin for a corner, which drifted through the box to the relief of the hosts.
While the visitors did not let up, Scotland soon began to settle in and they even had a chance to go ahead when Shaun Maloney saw his 11th-minute effort gathered by Thibaut Courtois.
It quickly became apparent that De Bruyne was going to be the one to watch for the home side, though, and they were nearly punished for failing to do so when the youngster fired a shot directly at Marshall after 26 minutes.
The goalkeeper could not keep them out for long, though, and just eight minutes before the half-time break, Defour beat him with an effort from just within the box.
It was just the 25-year-old's second goal for the team, his first coming in 2010, but it was credit to De Bruyne, who sped down the wing to feed him with a perfect cross.
And though the visitors could not double their advantage in the remainder of the first half, they came close early in the second as Nacer Chadli saw a long-range strike confidently stopped by Marshall.
The home side were struggling to assert themselves in front of goal and Strachan opted to hand a debut to 25-year-old midfielder Ikechi Anya in a bid to shake things up.
He immediately made an impact, too, beating his marker down the wing to set-up Maloney, who saw his effort fly narrowly over the bar.
The visitors then endured somewhat of a lull and there was more frustration as Nicolas Lombaerts had to be taken off after falling awkwardly.
But De Bruyne continued to excel and his stunning free-kick clipped the crossbar in the 84th minute.
In the final minute, Belgium got the second goal that their overall efforts deserved as Mirallas kept his cool to race past two defenders and beat Marshall with his shot.
Belgium will now need to beat Croatia on October 11 to ensure their place in Brazil in 2014.
