The game may well have hinged on two goal-line clearances by Yeovil in the first 12 minutes when the scoresheet was still blank.
On 11 minutes Jason Price beat goalkeeper Chris Weale to the ball, but his effort was cleared from the line by Nathan Smith for a corner and in the next minute Zak Whitbread's overhead kick was cleared away from under the bar by Danny Hutchins.
Yeovil began to settle down and as they pushed forward a free-kick from Andros Townsend was clutched at his far post by goalkeeper David Forde as a goal looked likely.
Yeovil did get the breakthrough on 40 minutes. Townsend put Kieran Murtagh away down the left and his pass picked out Jonathan Obika, who fired home low from ten yards.
It was the third goal in successive home matches for the teenage striker on loan from Tottenham Hotspur.
Yeovil got their second goal on 50 minutes. There was a dress rehearsal 60 seconds earlier when Paul Warne set up Gavin Tomlin, who fired wide of the far post. A minute later the same pair produced the same move and this time Tomlin's shot was fierce and inside the far post.
Yeovil almost got a third on 63 minutes when a free-kick from Gary Roberts almost caught Forde off his line and Town were now in control with the promotion-chasing Lions having lost their early sparkle.
Millwall's bad day was compounded in the 72nd minute when they had Alan Dunne sent off for a second booking both were for fouls on Townsend - another of the Yeovil trio on loan from Spurs.