Bowyer was charged for incidents which occurred during and after Charlton’s 2-1 defeat to Swansea City on October 2, as the Addicks squandered an early lead and the Swans moved top of the table.
Bowyer told Charlton’s official website: “I’m surprised and disappointed with the ban.
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“I didn’t shout or swear in my discussion with the referee but it is what it is. My focus remains making sure we are ready for Saturday’s game against Derby County.”
The three-match ban begins immediately, meaning Bowyer will be missing from the dugout for matches at home to Derby, and away to Bristol City and West Brom.
An FA statement said: “Charlton Athletic manager, Lee Bowyer, has admitted a charge of improper conduct and/or questioning the integrity of a Match Official and received a three match touchline ban and a £4,000 fine.