The game ended all square at 1-1 in normal time before the Trotters went on to win the shootout courtesy of three fine penalty stops by promising goalkeeper Chris Howarth.
Blackburn included former England striker Matt Jansen in their line up and there was also a place for James McEveley who spent part of last season out on loan with Gillingham.
Bolton took the lead from the penalty spot on 23 minutes after Rovers defender Craig Barr had upended James Sinclair in the area. Barr was dismissed for a second bookable offence and captain Joey O'Brien confidently struck the resulting kick past Steven Drench in the Blackburn goal.
Drench then made a fine save to deny defender Jarostaw Fojut from increasing Bolton's lead as he tipped over a thunderous free-kick by the Polish youth international on 34 minutes.
The second half saw Blackburn test Howarth much more but it was Bolton who had the first opportunity of the final half when American striker Johann Smith was foiled in a one on one situation with Drench.
Rovers then had two chances to find an equalising goal but neither Gary Harkin nor substitute Joe Garner could make their efforts count. The Garner effort saw a special save from Bolton's Howarth.
Ten minutes from the end Rovers equalised in bizarre circumstances as Bolton's new Academy defender Mark Ellis put through his own net past a stunned Howarth. However the former Exeter City schoolboy was spared in extended time as Howarth made a couple of fine stops in the shootout.
Bolton Wanderers: Chris Howarth, Bradley Hill, Danny Stott, Dale Whitehead, Mark Ellis, Jarostaw Fojut, Joey O'Brien, Johann Smith, Scott Jamieson, Karl Luisi
Subs From: Rhys Powell, Sam Ashton, Matt Cassidy, Sean Mountford, Leslie Thompson
Blackburn Rovers: Steven Drench, Tony Kane, Gary Rowntree, Gary Harkins, Craig Barr, James McEveley, Ralph Welch, Brian Hodge, Matt Jansen, Keith Barker, Keith Treacy.
Subs From: Tareck Sakali, Zac Jones, Joe Garner, Ryan Woods, Rostyn Griffiths
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