An upsurge of Dons fans showed 1100 witnessing a torrid game.
However they were eventually able to cheer Wimbledonâ€™s eighth win of the season, although Wednesday more than contributed to their own downfall.
The Owls' Derek Geary played a major part in the Dons opener, after he was booked for a foul on Joel McAnuff two minutes before the break.
After being booked he interfered with the free-kick and the referee moved the ball forward 10 yards. From the right angle of Wednesdayâ€™s box Lionel Morgan rifled the free-kick beyond Kevin Pressman.
Morgan's first goal of the season as he made a comeback from injury condemned the visitors to their 13th without a clean sheet.
The first half was a tame affair with David Connolly and McAnuff missing easy chances and Wednesdayâ€™s lone striker Lloyd Owusu shackled by Kelvin Davis.
The Owls threw away an equaliser within a minute of restart. Shefki Kuqi's measured ball threaded through the back line for the oncoming Owusu, who mesmerised the goalkeeper but put his finish wide.
Wimbledonâ€™s first attack of the second period came in the 54th minute when McAnuff latched on to a long clearance behind the defence and was pushed to the ground by Leigh Bromby, who was shown a red card.
The seven man Wednesday defence became superfluous and in the 62nd minute Connolly started and finished the move for the Dons second goal. Helped by Nigel Reo-Coker and a dithering defence he had no trouble in claiming his 11th goal of the season.
Neil Shipperley may have been the executioner for the third goal but the combination of Jermaine Darlington and substitute Wayne Gray put Wednesday's heads on the block.
Darlington's cross from the right was deflected away and Gray crossed from the right for Shipperley to scoop the ball beyond Kevin Pressman from three yards out