A sensational strike from Southampton striker Sam Gallagher broke Rovers hearts in the final of the U21 Premier League Cup.
Against an older and far more experienced Saints side, Eric Kinder's young charges pushed them all the way once more in front of a crowd of over 12,000 at St. Mary's.
Like the first leg at Ewood Park a week ago there was little between the two sides as the opening half ended goalless.
But on 52 minutes the deadlock was finally broken, Ryan Seager firing home side after Harrison Reed's shot deflected into the striker's path.
However Rovers were behind just 17 minutes as a Bradley Bauress ball into the box deflected off defender Matt Targett and flew into the back of the net.
It looked to be advantage Rovers when Southampton were reduced to ten men on 88 as Reed saw red for two bookable offences, it was quickly followed by a huge penalty shout as substitute Hyuga Tanner looked to have been pulled back in the box, but the officials were unmoved.
Despite the extra man it was the hosts who struck the decisive blow four minutes into added time.
Sam Gallagher cut inside from the right and exchanged passes with Josh Sims before letting fly from 20-yards, David Raya had no chance as the ball flew into the top corner. A strike suited forA any stage.
To their credit Rovers never gave up and pushed their hosts further and further back in the closing stages, but they couldn't get that one final chance their play deserved.
The home crowd showed their appreciation for the lads in blue and white as they collected their runners-up medals, it had been a gallant showing from all concerned.
Ahead of the game Rovers made just the one change from the side that drew 0-0 with the Saints seven days ago. Devarn Green the man to miss out with the hamstring strain picked up in the first leg. Lewis Mansell, his replacement in the match at Ewood, stepped up from the bench to start.
The hosts named the same 16-man squad from the previous match with an unchanged starting XI.
The first half was as close a contest as was seen at Ewood a week ago, Rovers through Connor Thomson threatened early, whilst Ryan Nyambe at the other end had to get back with an important block to deny Sam McQueen.
On eight minutes an error from Rovers defender Sam Jones gave the home side a glimpse of David Raya's goal, but as Jake Hesketh swept the ball across the six-yard box the Rovers goalkeeper claimed Ryan Seager's close-range effort.
After those early jitters Rovers grew into the game and went close to taking the lead on 13. Captain David Carson saw his shot by Jason McCarthy, Dean Rittenberg crossed for Sam Lavelle at the back post, but his header was tipped over by Paulo Gazzaniga in the Southampton goal.
McQueen fired over from distance before Rovers twice denied the home side in quick succession, Raya with a smart stop from Hesketh, Jones brilliantly blocking Seager's shot on the follow-up.
At the other end Thomson saw a strike deflect wide and from the resulting corner Lavelle looked to have been punched by the Saints keeper as he missed his clearance but referee Antony Coggins ignored the shouts from those in blue and white shirts.
Lavelle then showed his defensive prowess to thwart Seager as he shaped to shoot, his block ensuring that the two sides would go in at the break all square.
Neither side made a change at the break but it was the hosts who came out the stronger of the two teams at the start of the second half.
Three minutes after the resumption striker Seager went close with a curling effort before he followed that up with a thumping free-kick that Raya did well to keep out.
But the Rovers goalkeeper could do little about the opening goal that came on 52 minutes. Harry Reed's forward ball deflected of Lavelle and straight into the path of Seager and he fired into the back of the net to open the scoring.
Rovers looked for an immediate response, creating a series of corners, but they were unable to make their pressure count.
David Carson, on the end of a robust challenge in the first half from Reed, came out for the second half, but on 57 minutes had to make way. 16-year-old Lewis Hardcastle the man on to replace.
Rovers continued to force the home side back and deservedly drew level on 69 minutes.
Like the Southampton goal earlier, there was a degree of good fortune as Bauress sent a cross into the box, Mansell rose to challenge before the ball deflected off unsuspecting defender Matt Targett and into the back of the net.
Targett himself went close to making amends just two minutes later with a free-kick 20-yards out, the defender bending his effort inches wide of Raya's near post.
A spell of pressure from the home side followed, but Rovers defended well. Two minutes from time the hosts were reduced to ten men as Reed received a second yellow card for a near-identical challenge on Lavelle to the one he was booked for on Carson in the first half.
Rovers had huge shouts for a penalty waved way right on full-time when substitute Hyuga Tanner appeared to be pulled back, the players appealed but the referee was unmoved.
With nothing to separate the two sides at the end of the 90 minutes and and with away goals not counting, that meant thirty minutes of extra-time would be required, but it was the home side who struck the decisive blow just four minutes in.
Forward Gallagher brushed past two Rovers challenges as he cut inside, exchanged passes with substitute Josh Sims, before blasting an unstoppable shot into the top corner of the goal. A strike worthy of winning any occasion.
As the match entered the final period of extra time there were tired legs on show as both sides misplaced passes.
Rovers could have gained a second own goal when a Mahoney ball in from the left was sliced goalwards by McCarthy, the Southampton captain fortunate to see the ball fly wide of goal.
In the closing stages Rovers threw Lavelle forward as they searched an equaliser that would take the game to penalties, Bauress put a free-kick narrowly wide, substitute Sam Joel denied by Gazzaniga but the flag was already raised.
Eric Kinder's young charges never stopped running, a Mahoney centre came out to Hardcastle but his effort was deflected for a corner kick. Raya came up for it but Mahoney's centre was easily dealt with and allowed the home side held out to claim the trophy.
It had been a valiant effort from everyone in a blue and white shirt, they can be rightly proud of their display on the big stage. In the end they were beaten by a goal worthy of winning any contest.
SOUTHAMPTON: Gazzaniga, Mugabi, McCarthy (c), Wood, Targett, Gape, Reed, Hesketh, Gallagher, Seager (sub Sims 90+3 mins), McQueen (sub Sinclair 77 mins).
Subs not used: Britt (GK), Slattery, Debayo.
Goals: Seager 52 mins, Gallagher 94 mins.
ROVERS: Raya, Nyambe, Doyle, Thomson (sub Joel 90+1 mins), Lavelle, Jones, Rittenberg (sub Tanner 74 mins), Bauress, Mansell, Carson (c) (sub Hardcastle 57 mins), Mahoney.
Subs: Crump (GK), Daly.
Goals: Targett (OG) 69 mins.
Booked: Lavelle, Nyambe, Bauress.