The Scottish international was given his marching orders in the 55th minute after a clash with Lions striker Steve Morison, Rovers twice having to come back to earn a 2-2 draw.
With the appeal lodged, Rovers now await a decision from the FA as to whether Grant Hanley will be eligible to play in Tuesday night's match at Ewood Park against Brighton & Hove Albion.
"We are waiting on the FA, we've lodged the appeal," said Bowyer. "It has gone in first thing this morning and we are hoping we get an answer if not by close of play today then certainly first thing tomorrow.
"At the time I didn't think it was a penalty and it was very interesting to hear Ian Holloway's comments after the game, he himself said he didn't think it was a penalty.
"These things happen, we've got to wait for the decision and then move on because it was costly."
Because Rovers are yet to find out if their appeal has been successful or not, preparations for Tuesday's game have had to be worked on with and without Hanley in the squad.
The Rovers captain only returned to the starting eleven after a hamstring strain at the weekend after missing the games against Huddersfield, Leicester City and Watford.
If the referee's decision is upheld then Hanley will miss two matches due to him having been sent off earlier in the season away at Wigan Athletic.
"We've had to prepare with and without him, we are now waiting for the FA," added the Rovers boss.
"For Grant especially, it is going to be a big decision from the FA and we hope that they see it from our point of view because even at the time, if it was a foul, Matt Kilgallon is there to clear. So we'll see."
Tickets for Tuesday's match against Brighton are currently on open sale priced from £15 Adults, £10 Seniors and £5 Juniors. Book online today at www.onerovers.co.uk
and collect your tickets from the Blackburn End collection point on the day of the game.