Christian Roberts was lucky not to get sent off for a foul by the away dug out, and got away with just a yellow card.
Milton Keynes took the lead after 17 minutes with a shot from Jon-Paul McGovern beating Peter Brezovan in the Swindon goal to make it 1-0.
Just before half time the linesman awarded Swindon a penalty after a foul on Paul Ince just inside the box. Jack smith took the kick and sent the 'keeper the wrong way to make it 1-1 going into the half time break.
Ricky Shakes replaced Jack Smith on 50 minutes who had go off injured.
Andy Caton was fouled in the box on 56 minutes, and with Smith no longer on the pitch Paul Evans took the penalty and scored to make it 2-1 to Swindon. This was his 4th goal of the season so far.
Swindon half on for the deserved win, although Milton Keynes did come close in the final minute of stoppage time when they hit the bar.
Overall another good game, and an important win which keeps Swindon top of the table on 21 Points going into Saturday's home game against Peterborough United.