Kevin Davies struck after 93 seconds against his former club in a first half dominated by Wanderers at Ewood Park.
Eagles was a constant menace alongside Jacob Butterfield and Lee Chung-Yong, the attacking trio operating behind a typically robust and effective Davies.
After making a series of saves, Paul Robinson was unable to prevent greater damage when he turned Eagles’ 61st-minute free-kick against the post to leave Lee with a close-range formality, before Jordan Rhodes headed Rovers to within touching distance of a scarcely deserved point eight minute from time.
Victory ended a run of four straight draws for Bolton, still unbeaten in six games under Freedman’s stewardship, while Blackburn must bounce back from consecutive defeats and a stuttering start to Henning Berg’s tenure when they make the short trip to face fierce rivals Burnley on Sunday.
For the opening goal, ex-Burnley winger Eagles shuffled in from the right flank amid boos from the home support to slip Kevin Davies beyond the Rovers backline and the 35-year-old lashed high past Robinson.
Twice before the half hour, Eagles brought impressive stops out of Robinson – driving low and venomously from 30 yards with his right foot before crisply volleying left-footed towards the far corner from the inside left channel.
Robinson had to save well from Eagles once more before the half was out, while also arching backward to tip Zat Knight’s deflected hook goalwards over after those in front of him failed to deal with Jay Spearing’s free-kick.
Berg’s men started the second period with greater purpose but Robinson remained their key man, requiring fingertips to keep a delicate 25-yarder from Jacob Butterfield out of the top corner.
The former England man’s next save was in vain – touching Eagles’ free-kick onto the post after Dickson Etuhu bundled over Blackburn’s tormentor-in-chief and springing gallantly to his left as Lee tucked home the rebound.
A woefully off-target 25-yarder from Danny Murphy brought further venom from the terraces and Robinson saved superbly again to deny Knight from a Spearing corner.
Stephen Warnock was alert to block Mauro Formica from close quarters and a lifeline belatedly arrived for Rovers when Colin Kazim-Richards, on for King, angled a ball from the left to the back post where Scotland striker Rhodes ghosted in to head his 15th goal for club and country this season.
A final chance fell to Rhodes via Murphy in stoppage time but he could not scramble home.