Bowyer was charged over an incident at the end the Championship match against Barnsley on 28 January.
The Rovers boss, who attended a hearing at Wembley Stadium, was also fined £3,000 by the FA, following an incident against Barnsley last month.
A statement from the FA read: "Gary Bowyer will serve a one-match touchline ban with immediate effect after he admitted an FA misconduct charge.
"The Blackburn Rovers manager was charged with using language and/or behaviour in or around the tunnel and/or dressing room area at the end the game against Barnsley on 28 January 2014 which amounted to improper conduct.
"Bowyer, who requested a personal hearing, was also fined £3,000."