Van Gaal opted to field a back three of Nathan Ake, Virgil van Dijk and Jurrien Timber for their UEFA Nations League encounter. Daley Blind and Denzel Dumfries start as the wing-backs for the game, with Malacia sitting on the bench.
The 23-year-old has been in fine form for Manchester United this season since joining from Feyenoord for £12.9 million, playing eight games.
Fans were left frustrated with the Dutch coach's decision to start Blind ahead of Malacia.
Manchester United fans took to Twitter to state that the 23-year-old deserved to get a few minutes.
A few Netherlands fans are also concerned that their side are at a disadvantage due to the former United manager's decision to bench the starlet.
Check out the best reactions across Twitter to Van Gaal's decision to bench Malacia:
Malacia has made five caps for Oranje in his young career. Blind, a former United full-back, meanwhile, is a more experienced campaigner who has made 92 appearances for the Dutch national team.
Louis van Gaal and Frenkie de Jong hail Robert Lewandowski ahead of Netherlands clash against Poland
The Dutch backline will have the tough task of handling Polish marksman Robert Lewandowski as the two teams lock horns in the UEFA Nations League.
While talking to the press ahead of the game, Van Gaal labeled the Barcelona no. 9 as the best player in his position.
"I think Lewandowski is the best striker in the world." (h/t Barca Universal)
Frenkie de Jong, Lewandowski's Barcelona teammate, doubled down on his coach's claims as he showered his praise on the Polish striker.
“He is one of the best players in the world and he is an all-round striker. He is strong, he can hold the ball, his technical ability is really good, he makes a lot of runs and he scores a lot of goals.”
Despite the mutual respect, the Netherlands team will have to concentrate on the task of handling the threat Lewandowski possesses.
Lewandowski has scored 11 goals and provided two assists in eight matches so far in all competitions.