Rovers suffered a rare home defeat as a late Tim Cahill goal saw Everton claim the points with a 3-2 win.
Mikel Arteta had given the visitors a fourth minute lead from the penalty spot after the Spaniard was brought down by the returning Ryan Nelsen.
Arteta would then go on to court controversy when he only saw yellow when he poked Morten Gamst Pedersen in the eye in a 19th minute flashpoint.
Rovers ended the first half strongly, particularly from Pedersen's set pieces, but they couldn't grab the goal their play deserved.
The second was slow to get going, but a Leighton Baines shot that struck the woodwork saw the game spring to life.
With 20 minutes remaining Rovers were back on level terms - and how - Steven Nzonzi getting his first Ewood goal with a stunning 30 yard strike.
Rovers weren't level for long however as substitute Yakubu arrived perfectly to head the visitors back in front. But Rovers' substitute Jason Roberts squared things up moments later, latching onto a Kalinić pass to fire home in fine style.
Rovers went looking for the winner, but they were caught at the death. The usually stable defence again found out as Yakubu got round the back to square for Cahill to apply the finishing touch.
Sam Allardyce made three changes from the side that held Manchester United six days earlier.
Ryan Nelsen replaced the injured Chris Samba, hamstring victim Brett Emerton saw place was taken by David Dunn, whilst Vince Grella dropped to the bench as the manager opted for Keith Andrews.
Making his first start since Bolton back in February, captain Ryan Nelsen had a first five minutes to forget as the visitors were handed the perfect start.
Just four minutes were on the clock when Mikel Arteta brought a ball down in the area and the New Zealand international lunged in. The Spaniard dodged to the right to avoid the challenge but his legs were taken leaving referee Andre Marriner with the easy decision of pointing to the spot.
It was Arteta himself who stepped up and sent Paul Robinson the wrong way with a drive into the right corner.
Rovers were slow out of the blocks, the visitors enjoying plenty of possession, but eventually the home side rose from their slumber and started to get their game going.
It was from the set pieces of Morten Gamst Pedersen that gave Rovers their best opportunities, a 12th minute corner causing mayhem in the area, but Tim Cahill just did enough to stop Nikola Kalinić and then David Dunn from turning the ball home.
The talking point of the first half centred around a 19th minute flashpoint in which Pedersen and Arteta went nose to nose. Both players saw yellow from the confrontation, but had Marriner seen Arteta poke a finger in the Norwegian's eye he'd have surely sent the Everton man to the stands.
The referee continued to frustrate the home side, David Dunn penalised in the area for standing his ground as Tim Howard failed once again to deal with a Pedersen kick, then a wild challenge from Tim Cahill on Dunn went unpunished to further infuriate.
Everton survived another scramble from a Pedersen corner, then vital blocks on Martin Olsson and David Dunn saw Rovers denied.
On the stroke of half-time Tim Howard saved from Keith Andrews who's shot from the edge of the area almost crept in.
In the Ewood Park sunshine the second half was slow to get going. Neither goal was tested until just before the hour mark when a cross from the right by Tony Hibbert was headed over by Tim Cahill.
Phil Jones then sliced a Louis Saha cross-shot as the visitors threatened a second.
Tim Howard was yet to be tested in the second half, Martin Olsson volleyed well wide from the edge of the area, whilst although his centre picked out Morten Gamst Pedersen unmarked at the back post, the Norwegian was offside as he headed the ball wide of goal.
Moments later and Rovers were breathing a sigh of relief as Leighton Baines smashed a long-range effort off the foot of the post. It was a fine strike from the former Wigan man but it wasn't a patch on what was to follow.
There seemed little on for David Dunn as he was forced inside to Steven Nzonzi, but the Frenchman took a couple of touches before unleashing an unstoppable effort that flew into the far corner of Tim Howard's goal, the American having no chance.
After a second half that was so slow, suddenly the game, and the crowd, was full of life.
Ryan Nelsen almost went some way to redeeming his earlier error when he headed a David Dunn free-kick, but the Rovers captain was unfortunate to see his header land on the roof of the net.
The first half had seen Rovers threaten time after time from throw-ins into the area, but it was Everton who got their noses back in front from one on 79 minutes.
Leighton Baines delivered from the left, Victor Anichebe flicked on for Yakubu, on as a substitute no less than 20 seconds earlier to beat Phil Jones to the ball to head home.
However, Rover were behind for just two minutes, and it was one of Rovers' substitutes who did the damage.
Again the ball was worked inside from the left flank, where Nikola Kalinić hooked the ball into the path of Jason Roberts who lashed the ball home from the edge of the area.
But there was to be one more goal to come and unfortunately for all connected with Blackburn Rovers it would be the visitors who grabbed it as the clock ticked towards 90 minutes.
Leighton Baines had time to pick out Yakubu in the area, he took the ball past Jones to square at the near post where Tim Cahill was well placed to tap home from a yard out.
Six additional minutes were ultimately played, but Cahill's decisive strike proved to be the difference.
ROVERS: Robinson, Salgado, Jones, Nelsen (c), Givet, Pedersen (sub Roberts 64 mins), Andrews (sub Hoilett 71 mins), Nzonzi, Olsson (sub Di Santo 90 mins), Dunn, Kalinić.
Subs not used: Brown (GK), Grella, Basturk, Chimbonda.
EVERTON: Howard, Hibbert (sub Yakubu 78 mins), Baines, Jagielka, Bilyaletdinov (sub Anichebe 69 mins), Saha (sub Yobo 90 mins), Arteta, Distin, Cahill, Neville (c), Pienaar.
Subs not used: Turner (GK), Senderos, Duffy, Wallace.
Booked: Pedersen, Andrews, Roberts (Rovers), Arteta, Distin (Everton).