The world's second-ranked side in the world went into the match at the Al Thumama Stadium on the brink of equalling the longest-ever undefeated streak in the group stages of the tournament.
However, for the first time since 1994, the Red Devils lost a round-robin fixture, succumbing to second-half goals from Romain Saiss and Zakaria Aboukhlal.
The opening goal was initially given to Abdelhamid Sabiri's, whose free kick caused confusion inside the Belgium penalty area, but it was later deemed that Saiss had made the slightest of touches with the inswinging set piece.
Morocco's victory - just their third in World Cup history - sees them sit on four points in Group F, in second place and only behind Croatia on goal difference.
Meanwhile, Belgium are a point further adrift in third and will have to rely on Canada defeating Morocco on Thursday if they cannot defeat Croatia.
Speaking after the contest, Martinez defended his team's defending from set pieces, instead preferring to focus on the lack of composure when behind.
Martinez is quoted by BBC Sport as saying: "It's a difficult result because the first goal affected the outcome a lot. It's a dead ball situation, we couldn't get our game going and it's a game that we need to understand. We need to be together and react in the next game. That's what happens in the World Cup.
"The way we defended the goal is the way we have been defending free-kicks for six years, that's not the issue. It's a good ball in, it's nothing to do with the set up. I think we had good moments but we couldn't get clear cut chances, we only had a couple of half opportunities and if you allow that goal to be conceded then it changes the game radically.
"At the moment we conceded the goal we lost our composure too much and we couldn't get ourselves back in the final third with more thought. We knew Morocco were getting bodies behind the ball and we couldn't break them down. The game went away from us the moment we conceded the goal.
"We need to make sure that we get stronger together and we'll get ready for the third game."
Belgium have now lost four of their 10 matches in 2022, their only notable victories coming against Poland and Wales in the UEFA Nations League.