The 44-year-old had been in charge at Ewood Park since May 2013 having filled the role on a caretaker basis on more than one occasion.
The Lancashire side have only won three games all season in the Championship, are 16th in the league.
Blackburn Rovers can confirm that manager Gary Bowyer has left the club," a statement on the club's website read.
"The owners felt that following a disappointing start to the season, they have to act in order to give the club the best chance of success in the remainder of the campaign."
Assistant manager Terry McPhillips, first team coaches Craig Short and Tony Grant, and goalkeeping coach John Keeley also left the club.
It has been reported that Paul Lambert, who was sacked as Aston Villa manager last season, is the club's first choice to take the job, and will look to appoint him during the international break.
Lambert has previously won promotion from the Championship to the Premier League with Norwich, before leaving to take over at Villa.
Blackburn meanwhile are the eighth club to sack their manager so far this season, with four of those sackings coming since the start of November.