Fresh from home triumphs over Wolverhampton Wanderers and Arsenal, a first half goal from Connor Mahoney was enough for all three points at the Checkatrade Stadium.
With the first team in action at Sheffield Wednesday on Tuesday night, Damien Johnson took a young side South, the majority drawn from the successful FA Youth Cup squad that face Chelsea at Stamford Bridge in the semi-final second leg this Friday night.
But after Jack Doyle and Joe Rankin-Costello had gone close, it was one of the senior members of the development squad that broke the deadlock on 13 minutes.
Rovers broke well with Doyle playing Mahoney in on goal, and he took on his marker before cutting in from the right onto his favoured left foot to fire beyond keeper Christian Walton and into the back of the net.
The home side looked to get back on level terms but just like in the win over Arsenal last Friday night, Rovers were resolute in their play and restricted the Seagulls to very little in front of goal in the first half.
Instead it was Rovers who had further opportunities to stretch their advantage. Anton Forrester firing just wide with a shot across goal, before Mahoney saw another well-struck shot blocked.
The second half followed a similar pattern with Mahoney again going close, whilst Forrester and defender Matty Platt were just off target with headed opportunities.
At the other end Academy keeper Andy Fisher was called upon to make a rare save to keep out a Dylan Barnett free-kick, but that was as close as Brighton got to troubling the Rovers goal in the closing stages as Johnson's young side saw the game out comfortably to claim the points and a league double over the Seagulls.
"It was a different test for us than the Arsenal game and another great one for the lad's development," said the Under-21s coach.
"I felt that we handled the conditions better than Brighton as the pitch wasn't the best.
"We started really well and scored a good goal and had we been smarter with our final ball we could have got the second.
"In the second half Platt and Forester were unlucky with the chances they had, whilst Andy Fisher in goal has hardly had a save to make.
"So there are plenty of pleasing aspects from the game, it is another win and another clean sheet."
Ewood Park plays hosts to the Under-21s next match. They face West Bromwich Albion on Monday 11th April, kick-off 7.00pm.
ROVERS: Fisher, Travis, Askew, Tomlinsom, Platt, Wharton, Mahoney, Rankin-Costello (sub Carson), Forrester (sub Mansell), Hardcastle, J. Doyle (sub Thomson).
Subs not used: C. Doyle, Crump.