The Iron midfielder latched on to Freddie Sears' ball into the penalty area to despatch a clinical finish beyond Hull goalkeeper Matt Duke when the game appeared to be heading for a goalless draw.
Scunthorpe bounced back from last week's 4-1 home defeat to Leeds with a spirited display in a typical derby encounter and have now won their last three away matches in the Championship.
Hull, who had their fair share of chances, are now without a win in their last seven league games and only goal difference prevented them from slipping into the bottom three.
Scunthorpe dominated the early exchanges and defender Michael Raynes went close to an early goal, only to head wide in the seventh minute when well placed in the six-yard box.
Raynes then popped up at the other end to block a 20-yard shot from Hull midfielder James Harper, while visiting goalkeeper Joe Murphy held Hull defender Anthony Gerrard's header in the 16th minute.
Hull then enjoyed a period of possession, but were unable to carve out any openings and it was Scunthorpe striker Freddie Sears who had the next chance, latching on to Michael O'Connor's cross, but firing a 12-yard shot over the crossbar.
Sears was wayward with a 25-yard effort soon after and then Hull striker Mark Cullen missed the target from six yards as both sides searched for a breakthrough.
Chris Dagnall and O'Connor both went close for the visitors with long-range strikes, while Gerrard again forced Murphy to hold a goalbound header and Cullen pulled his effort from 12 yards wide.
Hull midfielder Tom Cairney unleashed a blistering shot from 20 yards that flew over the crossbar four minutes in to the second half, but Scunthorpe responded and defender Eddie Nolan forced Hull goalkeeper Matt Duke into a full length save from 25 yards after cutting in from the left.
Scunthorpe went even closer in the 58th minute when Martyn Woolford hit the post with a thumping left-footed shot from similar distance and that prompted Hull manager Nigel Pearson to send on Richard Garcia and John Bostock for Jay Simpson and Kevin Kilbane.
Woolford was on target again, this time with his head, to force Duke into another fine save in the 66th minute as the visitors began to get on top.
Garcia and Scunthorpe striker Sears traded carbon-copy shots from inside the area that both goalkeepers held and visiting defender Niall Canavan flashed a header wide from O'Connor's corner.
Duke denied Sears again, while Murphy held on to Harper's angled effort from inside the penalty area as Hull pressed in search of a late winner.
Tigers player/coach Nick Barmby's 82nd-minute header forced the best out of Murphy, while Bostock and Gerrard both went agonisingly close for the Tigers in the 88th minute with a 12-yard shot and header respectively.
But it was the Iron who snatched all three points in the 89th minute. Nolan and Sears combined brilliantly down the left for the latter to cross and O'Connor drilled home a right-footed finish from inside the area into the bottom corner to clinch his side another away success.