The Belgian was seen to bend over to shout at City striker Aguero after the Argentine went down appealing for a penalty in the 39th minute of Sunday's Manchester derby in the Premier League.
Referee Michael Oliver opted not to point to the spot, but television replays of Fellaini's outburst prompted fierce discussion on social media about whether the midfielder had intentionally spat at Aguero.
However, Van Gaal absolved his player of any wrongdoing at his post-match media conference.
"I have heard that it is a question on social media, but already 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," he said.
"I don't think that he's a spitting figure."
Fellaini was cleared after being accused of a similar offence in last season's Manchester derby at Old Trafford, when Pablo Zabaleta was the alleged victim - also when laid out on the turf.
However, City manager Manuel Pellegrini insisted he knew nothing about the latest incident, claiming: "It's something I don't know about."
Aguero went on to score a 63rd-minute winner as City condemned United to a fourth successive league loss to their rivals for the first time since 1970.
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