Neil Kilkenny has had his red card transferred to Joe Garner, with the front man to serve an immediate three match ban.
The Club had appealed against the midfielder's red card on account of mistaken identity, but also on the subsequent transferred red card for wrongful dismissal.
The Club provided video and written evidence to The FA, including a statement from Port Vale's Antony Gardner who stated that Garner had not hit him.
However, The FA's disciplinary commission did not find this evidence enough to clear the PNE No.14, who will miss the home game against Bristol City and the trips to Wycombe and Crawley.
A Club statement after the verdict had been issued said: "The FA decision to ban Joe Garner is a complete shock given the evidence.
"The match referee and the assistant referee nearest to the incident say that they did not see anything. The assistant referee furthest away stated that he saw Neil Kilkenny commit an offence that he clearly did not commit. The Port Vale player involved in the incident put in writing that at no stage did Joe Garner strike him.
"We are therefore dumbfounded as to what basis the FA can decide to ban Joe Garner."
Manager Simon Grayson added: "We are hugely disappointed. We felt we had supplied sufficient evidence to think the decision would be overturned.
"I would like to thank Port Vale's Anthony Griffith for his co-operation in this manner, he has acted in a thoroughly professional manner, it's a shame the FA's panel were not willing to trust his word and come to a decision to clear Joe."