Yeovil recalled Andy Lindegaard from his loan spell at Weymouth to make his first start of the season - and he was the hero as the Glovers came from behind to win 2-1 at Huish Park.
Scunthorpe travelled with the intention of allowing veteran Peter Beagrie to run at Adam Lockwood and Gavin Williams, Yeovil's right sided players, who were both on four bookings.
The thinking was that they would not be too happy to fly in with their tackles if another yellow card put them out of the FA Cup tie with Liverpool on January 4.
Glover's boss Gary Johnson scuppered that plan, however, by leaving both Lockwood and Williams out of his squad.
He was already without key midfielders Darryl Way and Lee Johnson so it was a strange looking Yeovil line up, and one which for long spells looked like suffering a home defeat.
There were few direct shots at goal in the first half but it was Scunthorpe who got the one that mattered.
In the 37th minute they were awarded a penalty when Richard Kell was brought down by Hugo Rodrigues and Beagrie scored from the spot.
Yeovil's replay came late in the second half when Beagrie had departed with a hamstring problem.
It gave Lindegaard the chance to push up from the back and in the 71st minute he provided a cross for substitute Kirk Jackson to head in at the far post.
Yeovil snatched the winner on 82 minutes. Lee Elam did the work on the left and Lindegaard met the cross with an excellent finish.
The defeat ends United's 14-match unbeaten run and leaves the club 9th in the Division Three table, while the victorious home side rise to third at the expense of Hull City who drop down to fifth following a home defeat at the hands of Mansfield Town.