After the first team's despair at Wigan Athletic on Sunday, it was the turn of the Under-21s to lose it late on Monday night.
Eric Kinder's young charges had done well to battle back from going a goal down as Darragh Lenihan scored his first Rovers goal to cancel out Conor Grant's opener, but at the death defender Ibou Touray bundled the ball home from a corner kick as the visitors claimed the points.
Adam Henley got an hour under his belt on his return to action, but John O'Sullivan lasted only half an hour as he picked up an ankle injury.
The result was harsh on Rovers as they had more than matched their more experienced opponents, particularly with a much improved second half showing.
Under the Ewood lights it was Rovers who were quick out of the blocks, almost taking the lead on 11 minutes.
Darragh Lenihan's flick from a David Raya clearance upfield saw the ball through to Dean Rittenberg, but the 17-year-old striker was unfortunate to see his left-footed strike crash off the crossbar.
The Toffees went close with two free-kicks soon after, George Green firstly seeing his centre skim off the head of John Lundstram and behind, his second went the other way around the wall and deflected into the side-netting.
Those chances prompted a spell of pressure where Alan Stubbs' side were much the better, David Raya saving well from Conor Grant before good defending from Aaron Tumwa denied Chris Long a sight of goal.
Rovers were dealt a blow just before the half hour when John O'Sullivan limped off. The Irish Under-21 international had picked up a 5th minute booking for a rash challenge on 'keeper Russell Griffiths, injuring his ankle in the process. The midfielder tried to play on but was ultimately frustrated. He left Ewood Park with his right foot in a protective boot and will have a scan on Tuesday.
Everton continued to force the pace and but for a fingertip save from Raya would have taken the lead before the break. From Green's corner from the left, Ibou Touray rose above Raheem Hanley to head goalwards but the Rovers' keeper did well tipped over the bar.
Five minutes into the second half the visitors had an excellent chance to open the scoring from the penalty spot after Hallam Hope was clumsily brought down in the box by Yann Songo'o. But the Everton man shot tamely from 12 yards and David Raya saved well to his left.
Rovers responded with a chance of their own, Rittenberg getting the better of Tony Hibbert to pull back for Hugo Fernandez but Griffiths saved well.
The deadlock was broken on 58 minutes and it was the visitors who were celebrating. Conor Grant, who had only moments earlier been denied by Raya, hit a peach of a shot from the edge of the area that left the Spanish stopper grasping thin air as the ball flew into the roof of the net.
Rovers responded in the best possible manner. Great approach play from Rovers saw Bradley Bauress tee up Rittenberg but the striker's volley was just wide.
However on 68 minutes they were level, Devarn Green working the ball well before finding Rittenberg, his shot was saved by a diving Griffiths but Darragh Lenihan was on hand to turn and force the ball home.
With that goal Rovers sensed the chance to pick up only their second win of the season and went looking for another goal, Fernandez hitting a dipping drive that Griffiths did well to save.
But it was at the other end where the crucial goal would come in the second of three added minutes. A corner from the left was blocked on the line by Songo'o but from the ensuing scramble it was Ibou Touray who got the vital touch as the ball somehow squirmed it's way into the back of the net.
Almost immediately the final whilst blew to signal a disappointing end to the night for the Under-21s.
"The way we played in the second half the result is cruel because we didn't deserve that," said Eric Kinder after the match.
"We had to see the game through, we have to do it properly all the time, but we haven't done it, we played short passes and we've paid the price for it.
"If we learn from that in the future then that is fine, but if we don't then they are foolish."
ROVERS: Raya, Henley (sub Beesley 63 mins), Bauress, Daly, Songo'o, Tumwa, Fernandez, O'Sullivan (c) (sub Green 29 mins), Rittenberg, Lenihan, R. Hanley.
Subs not used: Urwin (GK), Edinho, Pero.
Goals: Lenihan 68 mins.
Booked: O'Sullivan, Lenihan.
EVERTON: Griffiths, Hibbert, Touray, Ledson (sub Jones 76 mins), McLaughlin, Kenny, Grant, Lundstram (c), Hope, Long, Green (sub C. Duffus 61 mins).
Subs not used: Hewelt (GK), Williams.
Goals: Grant 58 mins, Touray 90+3 mins.