A first half double from veteran striker Dean Windass inspired Hull to a third successive Championship victory.
The 38-year-old pounced for the visitors' opener, firing in from an acute angle after only four minutes.
Windass then doubled Hull's lead 12 minutes later, applying a close-range header following neat build-up play.
Despite a cool strike by Jonathan Forte on the stroke of half time, Scunthorpe have now failed to win in their last six home games.
Scunthorpe Nigel Adkins on Uriah Rennie's decision to deny his side a penalty:
"It was a clear penalty on Martin Paterson. The referee is standing 10 yards away and the player takes Paterson's ankle away.
"In the past two games the referee has been big enough to say he'd made a mistake, but will this one?"
"It wasn't a fair result, but it's the result that stands."
Hull boss Phil Brown:
"They threw everything at us and it was an ugly second half but we showed a lot of character.
"I've said to the lads that there are 30 points up for grabs between now and Christmas and I've said that it could make or break our season.
"It was important that we hung on and we're making progress. I think the fans are starting to see that."
Scunthorpe: Murphy, Cork, Crosby, Butler, Youga, Forte, Sparrow, Williams (Paterson 55), Hurst, Logan, Hayes (Ameobi 76).
Subs Not Used: Lillis, Baraclough, Taylor.
Goals: Forte 45.
Hull: Myhill, Ricketts, Brown, Turner, Delaney, McPhee (Dawson 84), Ashbee, Marney, Hughes, Campbell (Folan 79), Windass (Garcia 67).
Subs Not Used: Duke, Okocha.
Booked: Turner, Ashbee, Ricketts.
Goals: Windass 4, 16.
Ref: Uriah Rennie (S Yorkshire).