Goals from Izzy Iriekpen and a Terrell Forbes own-goal ensured the Iron maintained their storming start to the season.
Striker Paul Hayes was unlucky not to open the scoring after just four minutes with a shot that came back off the inside of a post.
Goalkeeper Asmir Begovic then saved well from midfielder Matt Sparrow before the home side finally made the breakthrough after 27 minutes.
Grant McCann steered a corner deep to the far post where skipper Iriekpen headed home his first goal of the season. Sparrow and Martyn Woolford both went close before Scunthorpe finally made it 2-0 after 63 minutes.
Cliff Byrne's deep right-wing cross was headed back into the area by Martyn Woolford and in the scramble that followed Yeovil centre-back Forbes turned the ball into his own net.