Phil Smith started in goal in place of Peter Brezovan. The first half was fairly uneventful, although Smith was the busier of the two 'keepers made made an excellent save mid way through the first half.
It was Swindon who took the lead first in the second half after 53 minutes after a mistake by ex Swindon defender Sean O'Hanlon allowed Simon Cox a chance at goal, but he passed to allow Billy Paynter to score.
Stirling got a goal back for Milton Keynes after 65 minutes from close range after a Milton Keynes corner.
The game looked to be heading for a 1-1 before in the final minute of normal time Craig Easton was fouled in the box. Simon Cox took the penalty and scored to make it 2-1.
Swindon held on for the final 4 minutes of injury time to come away with a 2-1 win.