Seagulls defender Shane Duffy headed in Oliver Norwood's corner against his former side to put the visitors ahead.
Dale Stephens' volley after the break doubled the lead before Rovers' Sam Gallagher fired in from close range.
Brighton substitute Glenn Murray chipped in to seal the win after Blackburn's Gordon Greer was sent off, before Gallagher grabbed a consolation.
Murray's 13th league goal of the season and first away from home this campaign, came after Rovers goalkeeper Jason Steele dropped Lewis Dunk's shot at the striker's feet.
Any chance of a comeback by the hosts had already been made more difficult at 2-1, when ex-Brighton captain Greer was shown a second yellow for a foul on Bournemouth loanee Murray 16 minutes from full-time.
Gallagher smashed in his ninth Championship goal this season and second of the evening after racing clear in stoppage time, but it was too late for Owen Coyle's struggling side in front of a season-low crowd of 9,976 at Ewood Park.
Rovers have now lost 11 of their 21 Championship fixtures and Cardiff's win over Wolves ensured they slipped into the relegation zone.
In contrast, Brighton have been defeated in just seven of their past 68 league games in a run stretching back to May 2015, but will be replaced by Newcastle at the summit if the Magpies win at Wigan on Wednesday.
Duffy, who arrived on the south coast in August, has now scored four times against Rovers this season - three of them own goals.
The 24-year-old turned into his own net in a 3-0 defeat at Wigan on 13 August.
Four days later Duffy scored two first-half own goals and was then sent off in stoppage time in a 2-1 loss at Cardiff - his final league match for the Lancashire club.
Blackburn manager Owen Coyle told BBC Radio Lancashire:
"I thought we started the game really well on the front foot against a team I would say along with Newcastle look very, very big favourites certainly for automatic promotion.
"We certainly made one or two chances, but we accepted they were very dangerous on the counter-attack. At 2-1. We felt we were right back in it with a chance to turn the game on its head.
"But, it's a huge turning point when Gordon picks up the second yellow card. There was certainly contact and it leaves us with 10 men against one of the most difficult sides to face.
"They battled away and kept going, giving everything they could. There's plenty of heart and plenty of spirit, but we're conceding far too many goals.
Brighton manager Chris Hughton told BBC Sussex:
"That was closer than what we deserved and what it should have been. That's my only disappointment of the night.
"But, I thought we broke really well at times and at certain stages of the game, we could have been really out of sight.
"Ultimately, it's about three points and every away victory is a valued victory. No games are easy on the road so I'm delighted with the three points."
Match ends, Blackburn Rovers 2, Brighton and Hove Albion 3.
Second Half ends, Blackburn Rovers 2, Brighton and Hove Albion 3.
Foul by Craig Conway (Blackburn Rovers).
Glenn Murray (Brighton and Hove Albion) wins a free kick in the attacking half.
Goal!  Blackburn Rovers 2, Brighton and Hove Albion 3. Sam Gallagher (Blackburn Rovers) right footed shot from the right side of the box to the bottom left corner. Assisted by Liam Feeney.
Attempt saved. Steve Sidwell (Brighton and Hove Albion) right footed shot from outside the box is saved in the centre of the goal. Assisted by Solly March.
Substitution, Brighton and Hove Albion. Solly March replaces Anthony Knockaert.
Attempt blocked. Danny Graham (Blackburn Rovers) left footed shot from outside the box is blocked. Assisted by Liam Feeney.
Darragh Lenihan (Blackburn Rovers) wins a free kick in the defensive half.
Foul by Glenn Murray (Brighton and Hove Albion).
Jiri Skalak (Brighton and Hove Albion) hits the left post with a right footed shot from the left side of the six yard box. Assisted by Anthony Knockaert with a cross.
Offside, Brighton and Hove Albion. David Stockdale tries a through ball, but Glenn Murray is caught offside.
Delay over. They are ready to continue.
Sam Gallagher (Blackburn Rovers) is shown the yellow card for a bad foul.
Delay in match Sébastien Pocognoli (Brighton and Hove Albion) because of an injury.
Foul by Sam Gallagher (Blackburn Rovers).
Sébastien Pocognoli (Brighton and Hove Albion) wins a free kick in the defensive half.
Substitution, Brighton and Hove Albion. Steve Sidwell replaces Sam Baldock.
Attempt missed. Glenn Murray (Brighton and Hove Albion) header from the centre of the box is close, but misses to the left. Assisted by Sam Baldock with a cross.
Attempt missed. Darragh Lenihan (Blackburn Rovers) header from the centre of the box misses to the left. Assisted by Craig Conway with a cross following a set piece situation.
Sam Gallagher (Blackburn Rovers) wins a free kick on the right wing.
Foul by Lewis Dunk (Brighton and Hove Albion).
Goal!  Blackburn Rovers 1, Brighton and Hove Albion 3. Glenn Murray (Brighton and Hove Albion) right footed shot from the centre of the box to the centre of the goal.
Attempt saved. Lewis Dunk (Brighton and Hove Albion) right footed shot from outside the box is saved in the centre of the goal.
Foul by Hope Akpan (Blackburn Rovers).
Jiri Skalak (Brighton and Hove Albion) wins a free kick on the left wing.
Second yellow card to Gordon Greer (Blackburn Rovers) for a bad foul.
Foul by Gordon Greer (Blackburn Rovers).
Glenn Murray (Brighton and Hove Albion) wins a free kick in the defensive half.
Attempt missed. Jiri Skalak (Brighton and Hove Albion) right footed shot from outside the box is close, but misses to the left. Assisted by Sam Baldock.
Substitution, Blackburn Rovers. Liam Feeney replaces Marvin Emnes.
Substitution, Brighton and Hove Albion. Glenn Murray replaces Tomer Hemed.
Darragh Lenihan (Blackburn Rovers) wins a free kick in the defensive half.
Foul by Shane Duffy (Brighton and Hove Albion).
Jason Lowe (Blackburn Rovers) is shown the yellow card for a bad foul.
Foul by Jason Lowe (Blackburn Rovers).
Bruno (Brighton and Hove Albion) wins a free kick in the attacking half.
Attempt blocked. Oliver Norwood (Brighton and Hove Albion) right footed shot from outside the box is blocked.
Foul by Gordon Greer (Blackburn Rovers).
Tomer Hemed (Brighton and Hove Albion) wins a free kick in the attacking half.
Brighton went top of the Championship and made it 15 games unbeaten with a win at 10-man Blackburn Rovers.