Falcao, on loan from French club Monaco, scored in United's last league game against Stoke City and had begun to look sharp, but was not even on the bench as United toiled to respond when trailing 1-0 against a disciplined Southampton.
Asked afterwards for an explanation, Van Gaal said he had been forced to have several defenders on standby because of concerns over the fitness of Luke Shaw and Daley Blind.
Yet he still had young striker James Wilson on the bench, rather than Falcao.
"You have to compare players before the match. After the match you can say if a player should participate and you could have won, but you shall never know," van Gaal said during a tense post match press conference.
"I decided he is out of the 18 because I have to change Luke Shaw and Angel Di Maria for example. You have to look at the needs of your selection at the time. Marouane Fellaini came in and because of his substitution we created three chances."
The result pushed Manchester United down into fourth place, below Southampton.
Southampton manager Ronald Koeman said earlier this week Manchester United should be challenging for the title after spending 150 million pounds over the summer.
But it was a new face at Southampton, Serbian Dusan Tadic bought from Dutch side Twente in the summer, who proved the difference between the two sides and eclipsed United's British record signing, the near 60 million pounds Angel Di Maria.
Koeman talked up Southampton's Champions League qualification prospects after the result and said a draw against Chelsea and a win over Arsenal during the festive period had grown belief among the players.
"I am not surprised that we won today, because I know the players. I know the organisation in the team. We have 11 clean sheets now by 21 games, I think if we keep the sprit we can keep in front in the table," he said.
(Reporting By Susanna Twidale; editing by Martyn Herman)
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