The Red Lions shot into the lead in the first half through Tanguy Cosyns. They extended the lead via Emmanuel Stockbroekx in the 20th minute.
The Dutch hit back through Jelle Galema close to first half to leave the contest interestingly poised at half-time.
The second half did not produce any goals as Belgium pulled off a famous win ahead of the 2014 World Cup beginning in The Hague, Netherlands from May 31.
Belgium had earlier played out a 2-2 draw with Olympic champions and hosts Germany in their first game. The home once again split points in their second tie settling for a 2-2 draw with England.
England had lost their first game to the Netherlands 1-3.