The Manchester United midfielder was seen to bend over and shout at City striker Sergio Aguero during Sunday's Premier League clash after the Argentine went down appealing for a penalty in the 39th minute.
No spot-kick was awarded by referee Michael Oliver, but the strong reaction from Fellaini received close attention on social media, with replays inconclusive.
United manager Louis van Gaal rejected any claims that the 26-year-old had done anything wrong in the incident during his post-match media conference at the Etihad Stadium.
"I don't think he's a spitting character," said the Dutchman. "Sometimes when you shout there's a little bit of saliva [that comes out] with it."
Fellaini himself reacted on Twitter on Monday by suggesting the furore had been invented by the media and the FA has now confirmed that no investigation will take place.
It is the second time that Fellaini has faced spitting allegations against City, the first coming last season at Old Trafford following an altercation with Pablo Zabaleta, but again no action was taken against him.
