Alan Shearer scored twice to become the first player to reach 30 or more goals in a 38-match Premier League season.
Having netted 34 and 31 goals in each of the previous two campaigns, Shearer's brace at Ewood Park took his tally to 31 in the first season since the competition was cut to 20 teams.
Goals from Robbie Earle and Marcus Gayle had cancelled out Shearer's double, but Graham Fenton got the winner to move Blackburn up to sixth.
Wimbledon were 14th, where they would finish the campaign.
Paul Scholes's goal deep into stoppage time kept alive Manchester United's hopes of an unprecedented fourth consecutive Premier League title.
The midfielder's header with 20 seconds left of added time took Sir Alex Ferguson's side to within a point of leaders Chelsea.
The Blues would lose at Tottenham Hotspur later in the day but went on to win each of their remaining three matches, by an aggregate score of 17-0, to beat United to the trophy.