Victory over Poland on Friday (AEST) meant the Oranje only needed to avoid a heavy defeat to their neighbours at the Johan Cruijff ArenA in Amsterdam to seal top spot in Group A4 and progress to the UEFA Nations League Finals next year.
A result of that nature never looked like materialising, with Virgil van Dijk securing three points for the host in the 73rd minute – the centre-back's sixth goal for his country, four of those being headers from a corner.
The result extended Oranje's unbeaten run to 15 games (11 wins, four draws) since Van Gaal was reappointed for the third time in August last year, while it also saw Van Gaal move level with Dick Advocaat as the manager with the most wins in charge of Netherlands (37).
"We lost the ball so much and in simple situations," he told NOS. "Just like against Poland, only now even more.
"That also had to do with Belgium, who put more pressure on the ball, especially in the second half. We certainly didn't play our best game.
"Belgium are very strong in terms of quality. They have a lot of individual quality. [Kevin] De Bruyne and [Eden] Hazard; those are top players. The Belgians did very well from the back. They were the better team today.
"I told the players that we played very badly, but we didn't give away many chances.
"We also had the greatest opportunities, especially at the end. I think [Steven] Bergwijn and [Davy] Klaassen should have scored.
"This is a disciplined victory and that's nice. Although we were second best for 90 minutes, we still continued playing our game and were disciplined."
Marten de Roon replaced the injured Frenkie de Jong in midfield and Van Gaal was pleased with how the Atalanta man contained De Bruyne.
"I thought [De Roon] was one of the better players," he added. "He gave few balls to the opposition and defensively picked up De Bruyne, who walked a little further away from our pit bulls. He did that very well."
One of those "pit bulls", substitute Tyrell Malacia, also received praise from Van Gaal, who said the Manchester United man also did well in shackling De Bruyne.
"I put him on the left of the central defence because De Bruyne played a lot on that side," Van Gaal explained. "It's better to have a pit bull like that instead of someone like [Daley] Blind who tries to solve it tactically.
"I had already discussed this with him the day before yesterday. The defensive work he did very well."