Pools literally ran the first half thanks to the dominance of Richie Humphreys and solid work by Michael Maidens, Adam Boyd and Lee Bullock, yet they found themselves one down at the break.
It was a totally different story in the second half as Scunthorpe showed more mettle thanks to Matthew Sparrow and young Irishman Andy Keogh dictating matters and giving energetic displays.
Hartlepool dictated the early stages and inside three minutes Maidens rattled in a shot from 35 yards which Paul Musselwhite was pleased to parry.
Shortly afterwards Bullock burst through and the keeper again saved this time at his feet to prevent the opening goal.
It took Scunthorpe a long time to string anything together and when they did it was Keogh and Sparrow who were the architects.
The visitors were unlucky in the 37th minute following a neat move which saw Chris Llewellyn lay the ball back for Steve Turnbull who struck a brilliant shot that literally shaved the far upright.
Scunthorpe turned the game on its head two minutes before the break and went ahead against the run of play.
Richard Hinds slipped the ball to Cleveland Taylor who hooked it into the middle where Ian Baraclough headed home.
Poo'ls luck was out as they hit back sharply and from a corner Boyd's shot rattled the woodwork.
The Iron showed more steel as the second half got under way and Keogh set up an easy chance which Taylor spurned and then the Irishman flashed a speculative shot which went over.
A second goal in the 71st minute settled Scunthorpe down. The industrious Sparrow headed home Taylor's cross and in the closing stages Baraclough forced a flying save from Dimitrios Konstantopoulos.