Scunthorpe claimed their first away victory since 1 October as Hartlepool lost their ninth home match in a row.
The Iron went ahead when Garry Thompson burst forward and his clipped cross was turned in by the advancing Sam Togwell.
Scunthorpe doubled their lead as they counter-attacked from a Hartlepool throw-in as Thompson raced 50 yards and shot past goalkeeper Scott Flinders.
Pools pulled a goal back with seven minutes left through Andy Monkhouse's 25-yard shot but it was not enough.
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Hartlepool United head coach Neale Cooper told BBC Tees:
"I don't want to put pressure on the players but we've got to play a lot better than that for the supporters.
"I'm really sorry for the performance. I wanted to come back to see a good game of football and a good performance.
"It wasn't to be, so it's back to the drawing board and see what we can do."
Scunthorpe United assistant manager Chris Brass told BBC Radio Humberside:
"In order to win a game of football you do have to go that extra yard, it doesn't matter whatever level you're playing at. They did that today and I believe that's why we won.
"Performances like that really set you in a good stand and going into the turn of a new year it really has helped.
"The potential is there. They've got to start believing in themselves and they've got to understand what it takes in order to turn it around. It will take time."