Scunthorpe had the first chance after 10 minutes through former Swindon striker Leon Clarke, but his header went over the bar.
The home side took the lead on 18 minutes when Simon Ferry cut back for Paul Benson, who squared for James Collins to slot home from five-yards.
Midway through the first period Swindon should have doubled their lead when Matt Ritchie found himself clear on goal but goalkeeper Sam Slocombe spread himself to save well.
Paolo di Canio's side were down to 10 men after 33 minutes when defender Aden Flint was dismissed for a second yellow card.
Scunthorpe equalised after 56 minutes when Mark Duffy swung in a cross and Karl Hawley rose to head into the corner.