The on-loan midfielder was sent off on the hour mark for an altercation with Lee Williamson in the middle of the pitch, a scuffle which also resulted in the North End midfielder being given his marching orders.
Referee Phil Dowd dismissed the pair for violent conduct after an alleged headbutt during the incident, an offence that carries a three-match ban.
As it stands, Bowyer will now sit out the final game of the season at Reading on Sunday, as well as both legs of a possible play-off semi-final should Birmingham find themselves out of the automatic promotion places.
A Football Association regulatory commission will meet on Tuesday afternoon to discuss the submitted written and DVD evidence.
The Blues face the possibility of the current three-match ban being extended should the panel deem the appeal to be frivolous, although that would only affect Birmingham if they drop into the play-offs, as Bowyer's loan ends in the summer.