Eddie Nolan put the Iron ahead on the stroke of half-time before Michael O'Connor looked to have sealed the points late on. However, Boro hit back immediately through substitute Josh Walker to set up a tense finale.
Scunthorpe had the better of the first half and deservedly went in front. It was two minutes into stoppage time when Garry Thompson touched the ball neatly to Nolan and he crashed home an unstoppable shot from just outside the box.
Chris Day had been by far the busier of the two keepers. The Iron had twice gone close but Day came to the rescue as he saved from Shane Duffy and Oliver Norwood.
At the other end, Sam Johnstone saved well from Scott Laird's driven shot.
After the break the heat appeared to take its toll and chances dried up somewhat, although Mark Roberts went close for the hosts when he saw a crisp drive fizz just past the post.
The visitors effectively wrapped up victory in the first minute of stoppage time as O'Connor guided home a neat shot to make it 2-0, although Stevenage did have the last word as Walker pulled a goal back to set up a frantic finish.
Source: DSG