Rovers took the lead after 13 minutes when former Liverpool schoolboy Ralph Welch fired a 25-yard effort into the bottom left hand corner of Sam Ashton's goal.
Within ten minutes Gary Bowyer's team further increased their lead thanks to a neat shot on the turn by striker Keith Barker. Both he and fellow striker Joe Garner were proving to be a bit of a handful for the Wanderers centre backs Jaroslaw Fojut and Mark Charlesworth.
Just a couple of minutes later in the 25th minute Bolton pulled a goal back through England youth international Robert Sissons. The young midfielder had the simple task of tapping the ball in from a few yards out after Wanderers had two initial efforts foiled by Rovers keeper Zac Jones.
The Trotters also had the ball in the net prior to their goal, but the attempt was flagged offside by assistant referee Mr Bacon.
Blackburn had the upper hand and physical presence over their Bolton counterparts, but the home side did well to draw on level terms shortly before the break when Polish youngster Jaroslaw Fojut headed home an inswinging corner from the left.
The second half saw Rovers dominate for long periods but the Wanderers striker Karl Luisi worked tirelessly up front on his own for Bolton but sadly it was with little success as he found that Blackburn defensive duo Craig Barr and Eddie Nolan were in good form.
Rovers increased their lead on 55 minutes when Joe Garner converted from close range following a good move which down the left which involved his fellow striker Keith Barker.
Trotters coach Jimmy Phillips introduced a couple of substitutes in an attempt to get an equaliser, and one of his changes nearly paid off as striker Sean Mountford went close.
Joel Byrom had an effort for Blackburn which just dipped over the crossbar of the Bolton keeper Ashton. Despite a spirited effort by Bolton it is Blackburn who take all the honours this evening.
BOLTON YOUTH ACADEMY: Sam Ashton, Rhys Powell, Danny Stott, Dale Whitehead, Jaroslaw Fojut, Mark Charlesworth, Robert Sissons, Bradley Hill, Karl Luisi, Luke Magill (Sean Mountford), Craig Knowles (Matt Cassidy).
SUBS NOT USED: Kevin Connolly, Michael Roddy.
BLACKBURN YOUTH ACADEMY: Zac Jones, Tony Kane, Ryan Woods, Gary Stopforth, Craig Barr, Eddie Nolan, Ralph Welch, Bryan Hodge, Keith Barker, Joe Garner, Joel Byrom
SUBS NOT USED: Sergio Peter, Frank Fielding, Rostyn Griffiths, Raffaele DeVita, Mark King