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.
Reading 6/4, Birmingham 6/4, Draw 9/4