A last gasp Paul Hayes brace cost Notts County their first win in the Johnstone's Paint Trophy since 2001.
It looked in the bag for the Magpies, after Richard Butcher's ninth minute volley from just inside the Scunthorpe penalty area put them ahead.
Two stoppage time goals from Hayes prevented Notts' progression into the second round, first heading in a corner at the back post, followed by a second header moments later.
Although it is not the most glamorous competition, Ian McParland will be disappointed with his side's late concessions, especially with the 88th minute slip on Saturday against Shrewsbury denying them all three points.