United failed to register a single shot on target as they lost 1-0 and surrendered third place in the Barclays Premier League to the Saints, who earned their first away win at Old Trafford for 27 years thanks to Dusan Tadic's decisive 69th-minute goal.
Van Gaal selected Angel di Maria up front alongside Robin van Persie and then shifted Wayne Rooney up front after the former Arsenal striker suffered an ankle injury, while there was not even a place for Falcao on the bench.
That decision raised some eyebrows but the United boss insisted that he needed cover for other positions among his substitutes and defended his choice to drop the 28-year-old.
"As a coach you have to take decisions and you have to look at the composition of your team and your selection and you have to look at your game plan," he said
"Therefore I have to decide that he is out of the 18 because I have to change, for example, (Luke) Shaw and Di Maria.
"You have to look also to the needs of your selection at that time."
He added: "We have a lot of players who are coming back and (Falcao) has played the last five matches in a row."
Southampton manager Ronald Koeman was delighted to get one over his old adversary Van Gaal, but he was not so happy about Tadic's "stupid" goal celebration
The Serbian removed his shirt during the aftermath of his memorable winner and Koeman was clearly irked by the substitute's lack of restraint
"I don't like that," the former Holland defender said.
"It is a yellow card and a stupid fault
You get another and it is a red.
"When it is the last minute of the season and you have qualified for Europe, it is no problem
I don't like that
Keep your shirt on."
After losing the likes of Shaw, Adam Lallana and Dejan Lovren last summer, Saints were expected to struggle this season, but remarkably the south-coast club are now just 10 points shy of leaders Chelsea.
Koeman insists his team's Champions League aspirations are more than just a pipe dream.
"We know that we have a strong team and that was important in the end of December," he said.
"We got a point against Chelsea and the three points against Arsenal
That makes belief in the players
That is what you need if you are not a big club - belief in the players, not afraid of the name or the stadium
We learned that
"I am not surprised we won
We have organisation
If we keep the spirit and the organisation, we can keep in front in the table."
Source : PA