The 48 year old ex-Blackpool and Blackburn boss spent 11 months in charge of the Bantams after replacing David Hopkin.
Bowyer could not keep the club in League One last season and they have slipped out of the play-off spots as they chase a return to the third tier.
"Over the last few months, results have undoubtedly declined," said interim chief executive Julian Rhodes.
"In view of recent events, we felt a change was necessary in order to compete for a play-off place."
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