In a typically heated clash between two of English football's most bitter rivals, Fellaini became irate with City striker Aguero in an incident towards the end of the first half.
Aguero tumbled to the floor after Fellaini kicked his standing leg and the hosts appealed for a penalty, which was not given.
Fellaini clearly did not feel it was a foul and he bent down to shout at the Argentinian as he lay face down on the floor.
Some spit appeared to exit the Belgian's mouth as he unleashed his tirade at the striker, but Van Gaal insists it was not intentional.
"The TV has shown that he is shouting and sometimes when you shout there's a little bit of saliva (that comes out) with it," the United boss said.
"I don't think that he's a spitting figure."
Van Gaal's opposite number Manuel Pellegrini said he was not aware of the incident.
Fellaini played poorly at the Etihad Stadium, missing a good chance to snatch a point for United in the second half when he shouldered the ball wide when attempting a header.
Aguero, on the other hand, impressed throughout and scored the winning goal in the 63rd minute when he converted Gael Clichy's cross.
Source : PA
Source: PA