Goals from Byron Webster, James Hayter and in-form striker Paddy Madden racked up the Somerset side's eighth consecutive league win - and inflicted a first defeat in four games for the Iron.
The hosts dominated the early stages with top scorer Madden, Joe Edwards and Sam Foley all going close.
After Foley's curling effort was brilliantly saved, the Glovers made the breakthrough from the resulting corner, with Webster's stooping header sending the Huish Park faithful into raptures.
Scunthorpe were incensed just before half-time when Akpo Sodje ran through on goal and appeared to be hacked down by Webster, but referee Dean Whitestone waved away the protests and sent manager Brian Laws to the stands.
Yeovil continued to press in the second half with Hayter and the impressive Madden inches away from adding a merited second.
However, the points were soon secured when Hayter coolly converted from the penalty spot - Scunthorpe Callum Kennedy was adjudged to have fouled Sam Foley - before Madden notched his 18th goal of the campaign and his 10th in seven games, from close range.