Substitute Francois Zoko's dramatic injury-time goal earned Carlisle their fifth away win of the season.
Scunthorpe took an early lead when winger Andy Barcham curled a shot into the top far corner from an acute angle.
Carlisle then hit the post three times before midfielder James Berrett drilled a low shot into the far corner.
Scunthorpe substitute Jimmy Ryan and skipper Sam Togwell both missed golden chances before Zoko lifted the ball over Iron goalkeeper Sam Johnstone.
VIEWS FROM THE DRESSING ROOM
Scunthorpe manager Alan Knill told BBC Radio Humberside:
"You would take a draw when it goes so far into the game and yet we just switch off right at the end and it cost us.
"I thought there was a lot of positives and the only negative again is the result. But players are working really hard and trying their best but we just need to take some results at the moment.
"It's about winning and we need to win a game and I've got to say some of the performance was good, some of it wasn't, but there was some positives to take out of it."