Lee Ridley returned to the starting XI in place of the suspended Andy Dawson, while Jamie Forrester made his first playing return to Glanford Park as a Mudrat.
United dominated the opening half, following an initial sortie by the tigers when Tommy Evans did well to block an effort by Daniel Webb.
Problems for the visitors arose from a long throw by Lee Ridley which caused real panic in the ranks and then he forced a good save from Alan Fettis with a testing shot.
Striker Paul Hayes was crowded out before he could get in a shot, but the Iron maintained the pressure with Alex Calvo-Garcia having a long-range effort deflected by Justin Whittle and two further attempts received similar treatment.
Hull's Dean Keates saw Evans very alert to deny him and Whittle's header following a corner was punched away by the keeper.
City opened strongly after the interval almost grabbing a 49th minute lead when a low drive by Whittle was cleared off the line by Ian Kilford.
However, Scunthorpe went in front a minute later with a superb individual effort from Hayes who gathered the ball inside his own half and raced to the Tigers penalty box before firing home and beating of the attentions of two defenders.
Stung by this, Hull responded and it was a former Scunthorpe favourite Jamie Forrester who controlled well before turning to hook the ball over Evans after 66 minutes for his first goal for the Tigers.
Scunthorpe did not allow this to upset their rhythm and after Fettis had palmed away a Peter Beagrie cross the ball was met by Matt Sparrow, who headed in at the right hand post in the 76th minute.
Six minutes later Sparrow was on the mark again when he took on the City defence and powered forward to strike home a fine left foot shot for the third spectacular goal of the afternoon.
The defeat moves the Iron back into the top seven, but leaves the North Bankers staring in the face of another relegation battle.