With United trailing 1-0 at Preston North End in the FA Cup fifth round on Monday, Van Gaal replaced Radamel Falcao with Ashley Young, and pushed Fellaini forward to partner Wayne Rooney in attack.
The tactical switch paid off, Ander Herrera equalising before Fellaini and then a late Rooney penalty saw United through to a home quarter-final with Arsenal.
United have been accused of using long-ball tactics in recent weeks, but Van Gaal makes no apologies for playing to the strengths of the Belgian.
"I have used Fellaini a lot of times already - more than ever and he scores more than ever," Van Gaal said.
"He is a player that when we cannot beat the pressure with quality, we can always beat the pressure. That is a quality.
"Now I have played him for the first time in his [preferred] position but we have a lot of players who can play there.
"The whole team did it well because they believe also that we could do it with this shape.
"As trainer-coach or a staff, you can change the system but your players have to believe in it and perform it and that is not so easy and they do it and not for the first time. That is fantastic."
