Sam Winnall struck the crucial goal in the 77th minute, breaking free into the box to steer his shot past keeper Scott Flinders, after the visitors had looked likely to extend their five-match winning run.
In the first half, Pools were denied by two good saves from Sam Slocombe, keeping out efforts from Luke James and Jonathan Franks.
And in the second half Andy Monkhouse rattled the post with a deflected shot.
"We have got to take it on the chin and make sure we react to this defeat in the right manner," said Cooper.
"Credit to Scunthorpe. They defended their box well and you have got to give them a pat on the back for that. At the end of the day we did not quite do enough to win the game.
"I can remember we had a couple of good chances in the first half and hit the post in the second - but we did not do an awful lot apart from that.
"I did think we looked comfortably in control for much of the game - and unfortunately it was just one error of judgement from Christian Burgess that has cost us.
"He is devastated, but making mistakes is all part of the learning process for a young player. Christian has been terrific for us since joining us on loan.
"October has been a great month for us, apart from today. But we have just got to be humble in defeat and make sure we move on from it in the right manner."