It was suggested that the England international may get a further one game ban for appearing to argue with referee Phil Dowd after he dismissed him for throwing the ball in his direction towards the end of United's 2-0 defeat at Craven Cottage at the weekend.
Rooney was also seen to smack the corner flag in frustration at the decision as he made his way from the pitch after the incident.
However, the FA have confirmed that Rooney will not face any further action and the he will only have to serve the mandatory one game ban for his actions.
"We have clarified with Phil Dowd that there was no abuse from the player after he was dismissed," a statement from the Football Association reads.
"In relation to the incident when he punched the corner flag, the referee did not see that.
"We have written to Wayne Rooney reminding him of his responsibilities."