The Manchester United midfielder was given his marching orders after picking up two yellow cards against Birmingham on Saturday and afterwards Ferguson appeared to imply that Clattenburg had been inconsistent this season - but the FA decided his remarks did not cross the boundary to allege bias or impute the official's integrity.
An FA spokesman confirmed: "No action will be taken in relation to Sir Alex Ferguson."
The decision will come as a relief to the United boss, who has a two-match suspended touchline ban hanging over him after he questioned Alan Wiley's fitness earlier this season.
After Fletcher's red card at Birmingham, Ferguson said he had been "watching Mark Clattenburg this season".
He added: "As far as I'm concerned, I've not seen a softer sending-off for a long time. It is ridiculous.
"That referee did the Arsenal-Tottenham game earlier in the season and you needed to hit someone with an axe before he booked anyone in that game."
"There were some wonderful and weird decisions here."
Source: PA
Source: PA