Midfielder Sergio Peter got the eventual winning goal for Rovers on the hour mark after some fine determined play by team mates Keith Barker and Ralph Welch in the build up.
England youth international Robert Sissons had given Bolton the lead on 15 minutes when his well struck effort from the edge of the area had Blackburn goalkeeper Steven Drench well beaten.
Barker forced an immediate response from the visitors as he smashed the ball past Wanderers keeper Sam Ashton for the equaliser following good work by full back Andy Taylor.
Ashton then saved well to deny Rovers a second goal as he kept out an effort from Blackburn captain Gary Harkins.
Sergio Peter did eventually force the Ewood Park club into the lead for his first of two goals for the evening when converting a dangerous cross from fellow goalscorer Barker.
On 35 minutes Portuguese striker Ricardo Vaz-Te brought the hosts back on level terms as he rounded goalkeeper Drench for the equaliser to tie the scores at two goals each.
Experienced midfielder David Thompson tried to attempt a spectacular acrobatic effort but the former Liverpool and Coventry City star was to see his shot flash wide of Ashton's goal.
Peter eventually won the game for Blackburn with half an hour of the game to go but there where still chances for both teams to score more goals in the final quarter of an hour.
Bolton Wanderers Reserves: Sam Ashton, Bradley Hill, Sean Mountford, Dale Whitehead, Mark Ellis (Leslie Thompson), Jarostaw Fojut, James Sinclair (Matthew Cassidy), Robert Sissons, Bedi Buval, Ricardo Vaz Té, Johann Smith (Scott Jamieson).
Subs not used: Przemyslaw Kazimierczak, Mark Charlesworth.
Blackburn Rovers Reserves: Steven Drench, Tony Kane, Eddie Nolan, Craig Barr, Andy Taylor, Ralph Welch, Gary Harkins, David Thompson, Joel Byrom, Sergio Peter, Keith Barker.
Subs not used: Keith Treacy, Frank Fielding, Raffaele De Vita, Bryan Hodge, Mark King.
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