Rovers' development squad missed out on the chance to face Liverpool in the final of the Molson Coors Senior Cup after they were beaten by Fleetwood on penalties.
After the match at Ewood ended 1-1, Rovers came up short in the resulting spot-kicks, losing 4-3 after Willem Tomlinson and Lewis Mansell saw their efforts saved.
That the tie needed to be settled by penalties was testament to an outstanding first half goalkeeping display from Rovers' Andy Fisher.
The young stopper made a string of fine saves to ensure it would be goalless at the break, before Stefan Mols came off the subs bench to fire Rovers in front on the hour mark.
But Fleetwood equalised soon afterwards as Michael Donohue's cross found the back of the net with Alex Reid claiming a vital touch.
Both sides had chances to prevent the match going to penalties, but it was Fleetwood who would go on to prevail from 12-yards.
Damien Johnson may have named the same team that had drawn with Aston Villa a week ago, but they looked a different outfit as a lively Fleetwood Town side dominated the first half.
Just three minutes in Fisher was called upon to keep out the visitors with a brilliant save, denying Donohue from close-range after Tyler Magloire had been caught in possession, Reid unfortunate to see his follow-up rattle the post.
Play continued to be firmly towards the Rovers goal, Ashley Nadesan saw an effort deflect wide, before the experienced Jimmy Ryan's attempted lob went well off target.
With Fleetwood giving Rovers little time on the ball, the home side struggled to get their passing play going. But their best move of the first half saw Joe Rankin-Costello send a ball into the area from the right, Lewis Mansell was well placed, but he planted his header over the bar.
But that was a rare first half chance for Rovers as aside from a couple of long-range efforts that cleared the bar it was the Cod Army who were fully in control.
Fisher made an unbelievable stop to keep out Nathan Sheron, before Willem Tomlinson diverted a shot from Elliot Osborne off his own post and away.
The Rovers keeper then got down well to palm a 25-yard effort from Osborne aside, before pulling off a stupendous save to thwart Jack Sowerby. Reid again unable to make the most on the follow-up as he slammed a shot into the side-netting.
The last chance of the half unsurprisingly came Fleetwood's way, but again Fisher was there to deny them. A free-kick into the Rovers box saw the defence all at sea, Sheron, unmarked, fired goalwards, but the young keeper saved with his legs.
Both sides made changes at the break as Stefan Mols replaced Daniel Butterworth for Rovers, whilst Harrison Biggins came on for Jimmy Ryan for Fleetwood.
Rovers threatened with the first chance after the restart, but Mansell, on the stretch, just couldn't connect with Joe Grayson's ball to the far post.
The visitors responded as Nadesan brought down a ball over the top, but Fisher was there to save the striker's shot.
But despite having just about kept Fleetwood out in the first half, it was Rovers who drew first blood in the second on 60 minutes.
Lewis Thompson made good progress down the left before crossing into the area, however it was only cleared as far Mols and the young midfielder lashed the ball first-time into the bottom corner for his first goal for the development squad.
Rovers could have doubled their advantage soon afterwards as a Tomlinson cross picked out Mansell, but the striker glanced wide.
Instead it was Fleetwood who drew level. Donohue made progress down the left flank, and his high cross flew beyond the outstretched fingertips of Fisher and into the top corner of the net with Reid claiming the final touch.
Goal provider Thompson then went close with two long-range shooting opportunities of his own, the first flashing just wide, the second requiring a save from Crellin.
Then the Fleetwood keeper had to be alert to thwart Mansell after the striker chased his own ball forward, sliding to claim at the second attempt.
But on 82 minutes the visitors should have taken the lead. Donohue with a fine ball to the back post to where substitute Dominic Kerrigan arrived, but whilst he planted his header back across goal, it went a yard wide of the far post.
Then it was Rovers' turn with a chance of a winner as Rankin-Costello closed in on goal. Sub Callum Wright helped the ball into the path of Mols, but his attempted lob was deflected behind.
With the match ending all square it meant a penalty shootout to decide the victors, but the visitors had the early upper hand as Tomlinson missed Rovers' first spot-kick.
Fisher kept out Nadeson's penalty to even up the kicks, but after Gerard Garner scored Fleetwood's fifth it was left to Mansell to take it to sudden death but the striker saw his shot saved to ensure it would be the visitors who would progress.
ROVERS: Fisher, Travis, Thompson, Tomlinson, Magloire, Grayson (sub C. Doyle 72 mins), Thomson (sub Wright 83 mins), Hardcastle (c), Mansell, Butterworth (sub Mols 46 mins), Rankin-Costello.
Subs not used: Powell (GK), Evans.
Goals: Mols 60 mins.
FLEETWOOD: Crellin, Donohue, Maguire, Holgate, Sheron, Wallace, Ryan (c) (sub Biggins 46 mins), Osborne, Nadesan, Sowerby (sub Garner 72 mins), Reid (sub Kerrigan 72 mins).
Subs not used: Turner (GK), Mooney.
Goals: Reid 68 mins.