Scunthorpe were favourites to win this tie, taking the competition more seriously in fielding a full-strength side, but in the end they had to put in a battling, aggressive performance to overcome Peter Taylor's second string side, who were reduced to ten men through injury for much of the second half.
It was Hull who started brightly although things just were not going right for Jason Price who was thrust up front in the absence of the main strikers.
He missed an absolute sitter in the ninth minute after an unfortunate rebound in the Iron defence placed the ball at his feet ten yards out but he skewed his shot wide.
Minutes later Price headed wide again from Dean Keates' free-kick on the left of the box.
But after 13 minutes, against the run of play, Steve Torpey gave Scunthorpe the lead with an unstoppable shot from 20 yards after the ball had spun free to him in a moment of chaos in the Hull box.
Four minutes later an overhead kick from Ryan France went just over the bar after a good long throughball by Andy Holt, and just after the half-hour Daniel Webb missed a good chance when he fired a shot straight at Tom Evans in a one-on-one with the Iron keeper.
But Scunthorpe began the second half in much more attacking style, forcing City back and the Tigers suffered a major blow when an injury to Steve Melton reduced them to ten men with all the subs used.
But after 65 minutes the Iron defence fell asleep and allowed Webb to pick his spot and roll in a shot in off the post from 20 yards.
But despite a late rally by City, Matt Sparrow regained the lead for the Iron with a 12-yard shot and, right at the death, Steven MacLean claimed the third after his shot took a hefty deflection and looped over Alan Fettis.