The Football Association has handed Wigan boss Paul Jewell a £2,000 fine and a suspended two-game touchline ban after he admitted to improper conduct.
Wigan boss Jewell was infuriated by referee Dowd's decisions
Jewell was punished for confronting referee Phil Dowd after Wigan's defeat at Arsenal on 11 February, and has also been warned about his future conduct.
Jewell is also facing a separate charge of improper conduct and/or bringing the game into disrepute.
That charge relates to his post-match media comments after the same game.
He requested a personal hearing over the incident and has until 30 March to respond.
Jewell was furious that Dowd failed to give a penalty when Mathieu Flamini appeared to bring down Emile Heskey when Wigan were leading 1-0.
Jewell stormed on to the pitch at the final whistle to remonstrate with Dowd.
Wigan have complained to the FA and Premier League about Dowd's conduct.
I am going to get into trouble I know that, because I made my mind clear to the officials
Wigan manager Paul Jewell
Their complaint has also gone to referees' chief Keith Hackett, with Wigan claiming "that a number of their players were verbally abused in an aggressive and menacing manner by Mr Dowd".
Jewell has already announced he is determined to fight the charge and 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."
During the defeat at Arsenal, Dowd further infuriated Jewell by not letting Josip Skoko back on to the pitch after he had received treatment, meaning the Australian was still on the sidelines as Fitz Hall scored the own goal that set the Gunners up for a comeback win.
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Wigan's defeat left them in trouble at the bottom of the Premiership - and facing the expensive prospect of relegation.
Jewell said in the news conference after the game: "Dowd has cost our team the points - it could cost us £50m.
"I am going to get into trouble, I know that, because I made my mind clear to the officials."
Latics' owner Dave Whelan is also unhappy and has claimed Dowd swore at Wigan's players during the match - an allegation also made by Jewell.
The Wigan chairman said: "This particular referee seems to get it wrong quite a lot and surely they have to look at his performances over the season.
"He gave 10 yellow cards and there was only one foul all game.
"It is disappointing when you get a penalty that is such a nailed-on penalty and it is not given.
"You wonder what the hell goes on. Do they not like giving penalties at places like Manchester United and Arsenal?
"The referee used foul and abusive language to our players - that is not acceptable and we should take that up with the league.
"If the players used foul and abusive language to the referee, they would have been sent off."