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In a game that managed to be entertaining despite the constant whistle of referee Keith Stroud, Yeovil took the lead but lost it before half time.
They equalised at the start of the second half and for a long time 2-2 looked the most likely result.
But terrific Yeovil goals in the 82nd and 86th minutes clinched victory for the Glovers although the Iron had the last word when the lively Paul Hayes scored his second in stoppage time.
Yeovil went ahead on 16 minutes with a superbly taken goal by their big Polish striker Bartosz Tarachulski.
In the 36th minute a free-kick was flicked on by Steve Torpey and Hayes finished superbly.
Scunthorpe then grabbed the lead in first-half stoppage time when a right-wing corner from Ian Baraclough found its way to Andy Butler who finished clinically.
Yeovil came out for the second half looking as though they meant business and in the 47th minute levelled from a 20-yard free-kick when Tarachulski was fouled.
Manager's son Lee Johnson blasted a kick low through the wall past keeper Paul Musselwhite.
The league's top scorer Phil Jevons was not at his best for Yeovil and chances went begging but the introduction of substitute Rory Fallon - signed earlier in the day on loan from Swindon - proved decisive.
He headed in Johnson's corner on 82 minutes and when Arron Davies scored a terrific 30-yard effort four minutes later victory was secure.
United never gave up, however. Hayes knocked in his second goal four minutes into stoppage time and Yeovil then had to hang on to take the points.