Heartbreak struck for Latics as Ben Reeves tapped home deep into injury time, leaving Oldham pointless.
Adam Lockwood opened the scoring for Latics in the first half but a goal just after half time from Samir Carruthers levelled the scores, before Reeves' winner.
The home side grew into the game and went mightily close on 14 minutes. Hodson picked up a through ball and drilled a low cross into the box but no Dons player was attacking the ball.
With half an hour on the clock, Kusunga, who was booked earlier in the game, got on the end of a Jonathan Grounds corner but the defender headed wide.
Five minutes later and Latics were in front. Harkins' cross found the head of Lockwood, whose header creeped past the goalkeeper and into the bottom corner.
Buoyed by the goal, the visitors went in search of more before the break. Jon Stead was finding a lot of space behind the defense and forced a good save from Martin straight after the goal.
As the home side started to get restless, Latics looked to exploit with midfielder Harkins an instumental figure. His perfect delivery landed onto the foot of Danny Philliskirk but the forward's shot just deflected past the post.
Half time probably came at the wrong time for Latics as they were on top and soon after the break, the Dons equalised. Carruthers was allowed space to run in to and places his shot past Mark Oxley to level the scores.
Latics didn't let the goal affect and continued to attack. Harkins, Philliskirk and Jonathan Grounds had half chances without testing the goalkeeper.
The home side started to grow in confidence and only mid way through the second half, Kusunga received his marching orders for a second bookable offence. He pulled down a Dons player and the referee had no hesitation in producing the red card.
With Latics down to ten, MK Dons looked to exploit the man advantage. Antony Kay smashed an effort from 35 yards which narrowly went over the crossbar and the Lancashire side had to be alert as the visitors forced waves of corners but they dealt with them well.
With Oldham defending resolutely, Oxley produced a wonderful save with only five minutes of the game remaining. Reeves received the ball on the edge of the area and curled one towards goal but the goalkeeper tipped the ball away from danger.
The fourth official indicated a minimum of four additional minutes and deep into that, Dons found the winner. After Oxley saved the initial shot, the ball fell for Reeves who poked home from close range to give the Buckinghamshire side the win.