The 27-year-old was incensed by Atkinson's decision to award a late penalty to Villa for his challenge on Gabriel Agbonlahor, even though replays showed he played the ball.
Johnson said after the match on April 25: "The referee was a disgrace. He's ruined the match and clearly shouldn't be doing these kind of games - it was too big for him."
The former Cardiff and Wycombe centre-back was charged by the Football Association and at a personal hearing on Tuesday, he was fined £7,500 and warned as to his future conduct.
Johnson, who has been virtually ever present for Alex McLeish's side following his £5million move from Cardiff last summer, was not the only Birmingham player to find himself in hot water following the 1-0 defeat.
Captain Stephen Carr was given a one-match ban, which he has already served, after accepting an FA charge of improper conduct for a offensive gesture he made to Villa fans at the end of the match.
And the club have requested a hearing to put forward mitigation after accepting a charge of failing to control their players following the award of the penalty, which James Milner converted.