Ince, the Premier League's first British black manager, was in charge at Ewood Park for six months. Rovers have suffered six consecutive league defeats and sit five points from safety in the relegation zone.
"It is with great sadness that the board announce that Paul Ince is to leave the club," Rovers chairman John Williams said in a club statement.
"Three wins in 17 games has seen a squad, which finished seventh last season, fall to 19th position. We are currently in real danger in becoming detached from the pack.
"The survival of the club in the Premier League is paramount and our focus now is finding a replacement who will be able to maintain our top division status.
"Paul will bounce back, he is a fighter, and we wish him well."
Former England midfielder Ince, 41, was appointed on a three-year deal in June this year, replacing his former Manchester United team mate Mark Hughes who left to take over Manchester City.
Rovers began the season with an away win at Everton but picked up just two further league victories, the last in late September, as their form deteriorated and the final straw for the club's board came with a 3-0 defeat at Wigan Athletic on Saturday.
DESPERATE TO SUCCEED
Ince had asked for more time to get it right with games in the next 10 days against Stoke City and fellow strugglers Sunderland.
Williams said that the club "had been desperate for Ince to succeed" but told Sky Sports News that "it was time to change in order to help the club secure its status."
Ince, who also played for Liverpool and Inter Milan and won 53 England caps, led Milton Keynes Dons to the League Two title in his first season in charge this year after starting his full managerial career at Macclesfield Town.
Ince is the sixth Premier League manager to leave this season after Alan Curbishley, Kevin Keegan and Roy Keane quit West Ham United, Newcastle United and Sunderland respectively, and Harry Redknapp left Portsmouth to replace the sacked Juande Ramos at Tottenham Hotspur.
Blackburn said they were endeavouring to appoint a new manager before the home clash with Stoke on Saturday.
Former Rovers manager Graeme Souness is the bookmakers' favourite to replace Ince at Ewood Park, with former Bolton Wanderers and Newcastle United manager Sam Allardyce also linked with the position.
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