Gozie Ugwu, on loan from Premier League side Reading, struck twice late on after former Oldham pair Keanu Marsh-Brown and Reuben Reid had put the Glovers ahead at Glanford Park.
Scunthorpe are now one of two sides yet to register a point so far in the new season along with Leyton Orient, whose home game against Hartlepool was called off after the away side found themselves stuck in motorway traffic.
Yeovil, meanwhile, are joined on seven points from three games by three other sides including Tranmere Rovers, who left it late to snatch a 1-1 draw at Shrewsbury and maintain their unbeaten start.
Also in the top four are Stevenage, who won 1-0 at Oldham courtesy of Lucas Akins’ first-half penalty, and Paolo di Canio’s Swindon Town, who won by the same margin at home to Milton Keynes Dons thanks to Matt Richie’s winner.
Further 1-0 scorelines were found at Doncaster and Notts County, with both sides losing at home to Crawley and Walsall respectively.
Brentford ran riot over Crewe Alexandra at Griffin Park as braces from Clayton Donaldson and Farid El Alagui and one from Harlee Dean led to a 5-1 win, with Mathias Pogba scoring for the visitors.
There were another six goals to be found at Brunton Park, where Carlisle inflicted further misery on the Portsmouth fans who made the long trip up north in a 4-2 home win.
Preston North End and Sheffield United, both desperate to return to the Championship on their second attempts, were held 1-1 on the road by Bournemouth and Colchester.
And Coventry, who fell into the third tier this year, saw a two-goal lead go to waste as Bury clawed back for a point with a 2-2 draw at the Ricoh.