Standard Liege striker Michy Batshuayi grabbed the only goal of the game just before the interval to maintain his side's 100 per cent record, while Fulham's Liam Donnelly was sent off in injury time.
Stephen Robinson's side have now lost both of their Group Nine clashes but this represents a significant improvement on May's 3-0 reverse in Cyprus.
After a slow start, Northern Ireland drew a couple of saves from Belgium goalkeeper Thomas Kaminski, Carl Winchester and Josh Carson both trying their luck.
The hosts settled after that with Paul-Jose Mpoku, Thorgan Hazard and Yannick Ferreira-Carrasco coming into the game more but failing to work Connor Devlin.
Indeed, the next shot on target came from Oldham midfielder Winchester after 42 minutes but he could not beat Kaminski.
Instead, Belgium scored with their first real attempt on goal, Batshuayi firing home from Laurens De Bock's assist moments before the interval.
Dagenham's Sean Shields replaced Kirk Millar at half-time, the first of three replacements alongside Jamie Reid and Paul McElroy, but Northern Ireland could not find an equaliser.
James Gray saw his 56th-minute free-kick saved and soon after Batshuayi hit the woodwork.
There were chances at either end for a second goal but it did not materialise, and with three minutes of added time on the clock Donnelly picked up a second yellow card.