Wigan had looked set to inflict a first defeat on Arsenal at their Emirates stadium after leading through Denny Landzaat's first-half goal. But the Londoners scored twice in the last 10 minutes to keep the visitors deep in relegation trouble.
Jewell was furious Dowd failed to award Wigan, who are one place above the Premier League drop zone, a penalty when Emile Heskey tumbled under a challenge from Mathieu Flamini.
"We, as a club, will be fighting this (charge) tooth and nail," Jewell told Wigan's official Web site (www.wiganlatics.premiumtv.co.uk).
"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 I must take this all the way and that's what I intend to do."
Jewell said Wigan would be writing a letter of complaint to the FA, Premier League and to the head of referees Keith Hackett raising concerns about Dowd's behaviour.
Wigan alleged on their Web site that a number of their players were verbally abused in an aggressive and menacing manner by Dowd.