The midfielder cut in from the right and unleashed an fine left-foot shot from the edge of the box into the far corner past keeper Chris Day after 68 minutes.
It was out of character with what had gone before as Scunthorpe struggled to find a cutting edge up front despite dominating possession throughout.
Duffy himself had missed the best chance of the first half when he failed to find the net after bursting free into the box.
Leading marksman Karl Hawley was unlucky when he crashed an early second-half header off the bar as Scunthorpe kept up the pressure.
Stevenage were happy to fight a solid rearguard battle and had little to offer as an attacking force as they slipped to their fifth successive defeat.
Their one chance of the game came in the first half for Robin Shroot, who almost capitalised on an error from home centre-back David Mirfin but his effort was well saved by Sam Slocombe.