Dowd has has turbulent times refereeing the Latics and is reported to be rejected by a number of the big clubs who don't want him to referee their fixtures.
The referee's conduct has also been brought into question with a number of the squad claiming that Dowd sqore at them during the game.
Jewell said: "We, as a club, will be fighting this tooth and nail. We owe it to our supporters to fight this because if I just shrug my shoulders and do nothing when I feel an injustice has been done, it would be letting them down.
"I have been overwhelmed with the support I have had from inside the game, big figures who I respect a great deal. They have told me in no uncertain terms that I must take this all the way, and that's what I intend to do."
Time will tell if the FA wants to listen or continue to brush issues such as this under the carpet.