WATCH: Dons get dumped out of the Checkatrade Trophy
Despite leading after 24 minutes through a Alex Lacey own goal, Dons barely threatened but looked the better side at Huish Park.
But coming into the game eight undefeated, Yeovil came out fighting and were soon level when Paul Downing tripped Tahvon Campbell to give away a penalty, which Kevin Dawson converted.
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And when Daniel Powell was adjudged to have handled in the area, Francois Zoko fired the Glovers into the lead.
Samir Carruthers was sent off after picking up his second booking, and Yeovil made their numerical advantage count as Lacey made up for his earlier own goal but rattling home a third before Ben Whitfield completed the rout.