Saido Berahino, Lee Gregory and Barry Bannan gave the Owls a 3-0 lead in the first half before Tottenham Hotspur loanee Troy Parrott pulled one back for MK Dons before the break.
Though Darren Moore’s side were defensively disciplined throughout the second period, Scott Twine’s injury-time free-kick set up a nervy finish after the fourth official indicated there would be 10 minutes added on.
But fortunately for Wednesday the hosts couldn’t capitalise and they move up two places to fifth.
Scroll down for our player ratings.
5. Chey Dunkley - 6
Introduced in place of Dean in the first half for his first appearance since Gillingham. His first taste of the action saw him head a clearance into the path of an MK Dons player, who released Parrott for their goal. Not his first mistake this season, it has to be said. Always a threat in the opposition box, however. Photo: Steve Ellis
6. Jordan Storey - 7
Generally solid. Took one for the team with a booking for a clever foul on Twine in the second period. Photo: Steve Ellis
7. Jack Hunt - 6
Quieter going forward than usual but contributed to a generally decent effort defensively. Photo: Steve Ellis
8. Marvin Johnson - 7
A little quieter going forward than in recent weeks, but solid all night defensively. Got the better of Corbeanu during the former Owl's cameo from the bench, much to the delight of the travelling fans. Photo: Steve Ellis