Huth also received a retrospective three-match ban for pulling Fellaini's hair during the incident, which was missed by the match officials.
"Of course Fellaini has to control himself but I think most people would react in a similar way to being grabbed by the hair," Van Gaal told reporters.
"By also giving Huth three matches the FA are admitting it was a foul and therefore a penalty. That is disappointing for us but there is nothing we can do if the referee did not see it."
Fellaini will miss the rest of United's Premier League campaign, but will be available for the FA Cup final against Crystal Palace on May 21.
United are currently fifth in the table, four points behind Manchester City in the race for Champions League qualification and have a game in hand over their local rivals.
Van Gaal's team travel to Norwich City for Saturday's early kick-off and the Dutchman insisted that United could not afford any more slip-ups if they hoped to finish fourth.
"We have three games left and we have to win them all, beginning at Norwich City," he said.
"When you look at how we have performed against the top five this season and then the bottom five it is not a good average. Some of the smaller teams have done us big damage."
United travel to sixth-placed West Ham United after the Norwich game before ending their Premier League campaign at home against Bournemouth on May 15.
(Reporting by Nivedita Shankar in Bengaluru; editing by Sudipto Ganguly)
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