Paul Dickov fired Rovers in front from the spot early in the second half and substitute Craig Bellamy wrapped things up for the home side with a cool finish late in the game.
After Zurab Khizanishvili's red card against Liverpool had been overturned during the week, Mark Hughes was able to name an unchanged side.
Steve Bruce made four changes to the team that lost the local derby against Aston Villa last Sunday. Nicky Butt, Mikael Forssell, Stan Lazaridis and Kenny Cunningham all returned to the starting line-up while Blackburn-born David Dunn failed to make the squad.
Both sides started the game cautiously, with the ball never really making its way out of midfield.
As early as the third minute Emile Heskey picked up a booking for a dangerous tackle on Rovers captain Ryan Nelsen. After receiving treatment from the Blackburn physio, the New Zealand international was able to carry on, but was evidently hampered by his injury.
The whistle never seemed to be out of the referee's mouth from that moment on in what was ultimately a very disjointed first half.
Indeed the Ewood Park crowd had to wait until the 35th minute to see the first effort on goal. Morten Gamst Pedersen fouled Jermaine Pennant on the edge of his own box, but Jamie Clapham's left-footed free-kick deflected off the wall and out for a corner.
With chances at a premium, both defences had to remain focused and this was evident on 40 minutes.
Forssell found himself almost clear through on goal, and had it not been for a superb last-ditch tackle by Lucas Neill, the Finnish striker would surely have threatened the Rovers goal.
The best attempt of the half arrived just three minutes before the break. Khizanishvili played the ball forward for Dickov, and after Lazaridis had miscued, the lively Scot found himself one on one with the keeper, but his tame shot was easily saved by Maik Taylor.
With a mostly forgettable first half coming to an end, Rovers came out with a lot more drive and purpose about their play straight from the restart.
The warning signs were there for the visitors, as just a minute into the second half, Kuqi almost found Pedersen at the back post following a pin-point cross from David Bentley.
And less than two minutes later, Rovers got the break their endeavours deserved.
Kuqi flicked the ball onto Dickov inside the box and as Matthew Upson appeared to have hold of his shirt, referee Barry Knight pointed to the spot.
Despite the visitors' protests, which saw Blues captain Cunningham receive a yellow card, Dickov picked himself up and blasted home the resulting spot kick.
On 55 minutes, the Rovers strikeforce combined once against to create another good opening.
Michael Gray played a long free-kick forward for Kuqi, the big Finn headed the ball down to Dickov on the edge of the area, but his controlled volley fizzed narrowly wide of Taylor's right-hand post.
Both managers rang the changes, with Bellamy coming on for Dickov, while Jiri Jarosik replaced Lazaridis for the Blues.
And with just nine minutes left on the clock, it was the Rovers substitute who wrapped up the points for the home side.
After a mix-up in the home defence, Pedersen slid a perfectly weighted throughball for Bellamy and the Welshman, on his return from injury, calmly slotted the ball past Taylor.
MAN OF THE MATCH: Robbie Savage (Blackburn) - Had a big impact in a scrappy match against his former club with his wholehearted attitude a constant threat to the unconvincing City midfield.