Hughes was forced into one change from the side that famously defeated Manchester United at Old Trafford last Saturday.
Steven Reid slotted into the midfield in place of the suspended Robbie Savage, while Andy Todd was named amongst the substitutes following a four-game absence.
Bryan Robson made three changes to the team that lost 2-1 to high-flying Charlton last weekend.
Robert Earnshaw failed to make the 16, with Diomansy Kamara partnering Kevin Campbell in attack, while Martin Albrechtsen and Richard Chaplow replaced Steve Watson and Andy Johnson in the starting 11.
Both sides started well with Rovers registering the first effort on goal. Lucas Neill's ball into the box was instantly controlled by Paul Dickov, but his left-footed shot on the turn went harmlessly into the arms of Kirkland.
West Brom responded well and looked a threat down the flank.
On seven minutes, Albrechtsen burst down the right and supplied a superb ball across the face of goal, but Zurab Khizanishvili's faint touch prevented Campbell having an easy tap-in at the back post.
Four minutes later and again Albion broke with intent. Kamara bustled his way down the left, before pulling the ball back to Chaplow in the centre. The ex-Burnley man's effort was blocked, but when the ball fell kindly for Jonathan Greening three yards out, Brad Friedel was forced into a superb reaction save.
Rovers were dealt a cruel blow when Bellamy signalled to the bench that he needed to come off. The former Newcastle striker had only returned to the Rovers side for the game against his old club last month, after picking up a thigh injury while on international duty.
Kuqi was brought on to replace the Welshman and his arrival almost brought an instant reward.
David Bentley floated a ball in from the right, but after rising highest at the far post, the big Finn headed just inches wide of the visitors goal.
As the half progressed, struggling Albion looked much the better of the two sides, as Rovers failed to get hold of the ball.
With Savage a notable absentee and Tugay struggling to make an impression, it was left to Bentley to provide Rovers' biggest threat.
On 40 minutes, the England Under-21 international skipped past three Albion players down the centre before firing wide of the target from 20 yards.
Three minutes later and the former Arsenal midfielder again broke forward. He showed good skill to beat his man down the left, before looking to pick out Reid in the centre, but the Irishman was penalised for his challenge on Kirkland.
With the momentum now firmly with the home side, Hughes' men looked to make the breakthrough just seconds before the interval.
Michael Gray picked out Kuqi at the back post and when the substitute headed the ball down to Khizanishvili it looked certain he would score, but the Georgian's left-footed effort was deflected wide for a corner.
Rovers continued where they had left off in the first half and almost took the lead just two minutes after the break.
Pedersen found Kuqi down the right, who delivered a seemingly perfect ball into the box, but Albrechtsen somehow got there just in front of Dickov to steer the ball out for a corner.
Dickov was proving to be a real handful, as Rovers continued to press.
On 53 minutes, the Scotland international dragged the shot wide after a surging run and just six minutes later he believed he should have had a penalty after getting a push in the back by Curtis Davies
Pederson, Rovers' Old Trafford hero, was next to make the attempted breakthrough. After picking up the ball on the left the Norwegian winger cut inside two Albion defenders, but his shot on his weaker right foot was well blocked.
Much to the delight of the Ewood Park crowd, the breakthrough finally arrived in the 80th minute.
Kuqi's snap shot, following a clever backheel from Dickov, was deflected wide and from the resulting corner the flying Fin outjumped Neil Clement in the six-yard box to head home past Kirkland.
Rovers pushed for another and got the reward their second-half effort deserved two minutes from time.
After collecting the ball under pressure, Davies attempted to find his keeper, but the pass was considerably under-hit and Kuqi added his second of the game, slotting the ball through the legs of the on-loan Liverpool keeper.
Man of the Match: Shefki Kuqi - The big Finnish striker made all the difference after replacing Craig Bellamy early on in the game, gaining his reward with two goals to seal the victory.