Rovers crashed out of the Capital One Cup at the first attempt on a disappointing evening at Ewood Park.
Neal Bishop's first half header for the visitors was the only goal on the night to send Scunthorpe through.
The home side should have taken a 1st minute lead but David Dunn fired wide from close-range, whilst in the second half substitute Rudy Gestede's effort was harshly ruled out for a foul on the goalkeeper by Luke Varney.
Rovers huffed and puffed but the Iron defended stoutly to deserve their place in the next round.
Gary Bowyer opted to shuffle his pack for the visit of Scunthorpe United with ten changes from the side that drew with Cardiff City on the opening day of the season.
Jason Lowe was the only player to keep his place from the match against the Bluebirds, his reward the captain's armband.
Jake Kean returned in goal behind a back four of Lowe, Yann Songo'o, Jack O'Connell - making his senior debut - and Adam Henley at left back.
Ben Marshall, Lee Williamson, Chris Taylor and Luke Varney were the midfield men, with David Dunn operating in the space behind Josh King up front.
The visitors, making only their second ever appearance at Ewood Park, made two changes from the side that lost 3-1 to Swindon Town on Saturday. Naming a starting XI that included former Rovers youngster Eddie Nolan.
Rovers should have been in front inside 60 seconds as Josh King raced away from Miguel Llera and into the box, he squared for David Dunn but somehow he put his effort wide from five yards.
After that the home side offered very little as an attacking force as Scunthorpe were much the brighter of the two sides.
On 18 Jake Kean saved well from a drilled ball across the box from Gary McSheffrey, the second time the keeper had had to parry away from dangerous situations.
Jason Lowe was wide with a shot on the turn, whilst Ben Marshall saw a free-kick easily claimed by Sam Slocombe, but they were rare Rovers efforts.
Neal Bishop saw strong claims for a penalty waved away after a collision with defender Adam Henley, before Sean McAllister fired over from Paddy Madden's chest down.
Moments later the deadlock was broken and it was no surprise that it was the Iron who grabbed the opener. McSheffrey sending over a corner from the right to where Bishop rose unchallenged to head home.
A second goal almost followed from yet another McSheffrey delivery from the right, Chris Taylor blasting just past his own goal with a mis-hit clearance.
Just before half time Marshall cut inside to shoot left-footed but like the play from the home side in the first half, it lacked the purchase to test the opposition.
Gary Bowyer sent the same XI out for the second half, and like the first they almost scored with their first attack.
As Ben Marshall sent a free-kick over from the left, the ball curled over everyone and was heading towards the far corner until Slocombe's finger-tips pushed the ball behind.
Rovers then had claims for a spot-kick waved away as Yann Songo'o looked to have been held down as he attempted to get on the end of a Marshall centre, but referee Sebastian Stockbridge was unmoved.
Just past the hour mark Bowyer made a double substitution to try get back into the game. Rudy Gestede and Craig Conway replacing David Dunn and Ben Marshall. Almost immediately the pair combined as Conway's corner was headed over by Gestede.
Rovers thought they were level on 77 minutes only to see it chalked off. A Lee Williamson ball to the far side of the area was headed across by King, Varney got in front of goalkeeper Slocombe but as Gestede puts the ball in the net, the assistant referee flagged for a foul by Varney when it looked the other way around.
Varney and Gestede both saw headers claimed by the Scunthorpe goalkeeper as they pressed for a late leveller, but despite plenty of possession they couldn't make it count.
Had Dunn converted with the first chance of the game the match could have been different, but as it was, the visitors defended resolutely to ensure it would be their name in the hat for the second round.
ROVERS: Kean, Lowe (c), Songo'o, O'Connell, Henley; Marshall (sub Conway 62 mins), Williamson, Taylor (sub Cairney 78 mins), Varney; Dunn (sub Gestede 62 mins), King.
Subs not used: Eastwood (GK), Rhodes, Baptiste, Evans.
Booked: King, Williamson.
SCUNTHORPE: Slocombe (c), Nolan, Dawson, McAllister, Canavan, Madden, Myrie-Willilams, Bishop, Taylor (sub Addison 85 mins), McSheffrey, Llera.
Subs not used: Severn (GK), Sparrow, Hawkridge, Adelakun, Bateson, Wootton.
Goals: Bishop 34 mins.
Attendance: 5352 (including 551 visiting supporters).