A turgid first-half display in which United dominated possession against their third-tier opponents but failed to create a single clear scoring chance forced Van Gaal to act.
A goal behind following Scott Laird's 47th-minute strike, the Dutchman hauled off misfiring Colombian forward Radamel Falcao, replacing him with winger Ashley Young and pushing Marouane Fellaini further forward.
"Marouane Fellaini has a body, he also scores goals," Van Gaal told the BBC.
"I played him in the position that he wants for the first time but I do not always have a position for him. The spirit was better."
Three goals in the last 25 minutes justified the Dutchman's decision.
Young's quick feet created the equaliser for Ander Herrera and Fellaini arrived at the far post to meet Antonio Valencia's deep cross before knocking home the rebound.
Wayne Rooney, restored to the forward line after weeks playing in central midfield, darted clear to win the penalty which he converted to seal a comfortable win and set up a quarter-final clash with Arsenal.
Van Gaal has been criticised recently for reverting to long-ball tactics, with Fellaini as his target man.
The Belgian, signed by former United manager David Moyes for 27 million pounds ($41.5 million) in 2013, endured a difficult first season at United but has now scored four goals under Van Gaal.
The fans may not enjoy the route one approach but, with only one defeat in 19 games, it is proving to be a useful alternative for Van Gaal.
($1 = 0.6512 pounds)
(Editing by Nick Mulvenney)
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