Key to the change in fortunes was Yeovil caretaker boss Steve Thompson's decision to replace Nathan Jones and introduce striker Matt Harrold.
Harrold proved more than handful for a home defence that had to be reshuffled through injury and a sickness bug.
Home skipper Andy Crosby played for 70 minutes after pulling his groin in the warm up and did reasonably well but it was teenager Andy Keogh who took the honours with his work rate.
Harrold's contribution was immense as Yeovil grabbed their second away win of the season while Terry Skiverton and Liam Fontaine were key figures in their defence.
Yeovil were first to show, and when Fontaine got forward to swing a ball in from the left, Jones was there first but his header drifted wide.
As Scunthorpe settled down they began to force gaps in the Glovers defence and they took advantage in the 13th minute when Billy Sharp pushed the ball through and his strike partner Keogh smashed home.
Fontaine then stepped in smartly to halt a run into the box by Matthew Sparrow, but the Scunthorpe midfielder was instrumental in setting up the Iron's second goal in the 20th minute as he found Keogh who crossed to the far post for Sharp to convert.
However, what had looked comfortable for Scunthorpe soon evaporated as they allowed Yeovil to claw their way back.
Harrold stroked the ball through the middle in the 26th minute and the slight figure of Darren Way popped up to direct his shot home.
That was a shock and another followed in the 36th minute when Scunthorpe were caught napping from Fontaine's cross and Phil Jevons crashed in a left-foot shot.
Scunthorpe's young defender then forced Chris Weale to punch out a sharp drive and it flew just off target and then skipper Skiverton got in a fine header which forced Paul Musselwhite to move to his left swiftly to clutch the ball.
Yeovil took command immediately from the restart with Pablo Bastianini seeing a long-range lob fly over and then he wasted another effort by blasting over the bar.
However, the visitors went ahead for the first time when Harrold, who had proved a real handful, drove home in the 58th minute and then he made it four eight minutes later, driving a close-range shot under Musselwhite.
Scunthorpe responded and Sharp grabbed his second of the game in the 77th minute.
Keogh then had the ball in the net but was ruled offside and in the closing minutes substitute Wayne Corden cracked the ball against the bar but there was no fairytale ending for the Iron.