Two goals apiece from Dean Rittenberg and Jordan Preston confirmed the win for the visitors, with Wanderers’ attention now turning to Saturday’s home game against Aston Villa.
Blackburn started brightly with a goal after 15 minutes as Rittenberg opening the scoring, putting a firm header beyond Harry Campbell in the Bolton goal.
The visitors looked to improve on their lead before the half-time whistle, however had to be wary as Wanderers were starting to look a threat in the final third.
A couple of offside decisions went against Bolton but Guillermo Torres was able to slip under the radar, however Rovers were able to get back to clear the danger.
Moments later Wanderers’ Tom Walker managed to work his way past two Rovers players and get a dangerous low cross into the box but the outstretched Torres was unable to connect to worry Rovers custodian David Raya.
Bolton were pilling on the pressure looking for an equaliser and missed a great opportunity when Elliot Newby went through on goal, however the youngster’s finish was tame.
Despite a promising ten minute spell for the hosts, it was Rovers who grabbed the all-important second goal.
Unable to clear a Rittenberg cross, Preston was allowed time and space inside to stoke home into the bottom corner past Campbell.
David Lee’s youngsters looked to halve Rovers’ lead as Newby hit a low effort from the edge of the ‘D’ but Raya was equal to the effort.
Into the second half, and Bolton started the final 45 brightly and continuing to ask the Blackburn Rovers defence questions.
However, despite their valiant efforts, Rovers added a third as Preston fired a low effort into the bottom corner.
Wanderers managed to stem the flow of Rovers attacks but were unable to create any clear cut chances of their own, as the second half was largely contested in the middle of the park.
Rovers completed their scoring late with quarter of an hour to go when Rittenburg calmly finished past Campbell as the visitors travelled back to east Lancashire with three points.
After the game, academy coach David Lee said: “I am disappointed that we had opportunities to score but we didn’t take our chances.
“At 1-0 down we had fantastic opportunities to score but we didn’t and when you are playing against decent opposition, you will get punished.
"I am disappointed with the individual mistakes but players will make mistakes at this level and hopefully they will learn from it.
"They can’t keep on continuing to make mistakes because they have to learn from it sooner rather than later.”