The O’s had taken a first-half lead at stadiummk through a Dean Lewington own goal and looked to be progressing into the second round before a Mathieu Baudry own goal levelled the tie on the 88th minute. MK Dons then snatched the win in added time when Carl Baker drilled a low effort past Alex Cisak.
On the back of their opening day victory Orient made four changes to the starting line-up which saw Alan Dunne, Blair Turgott and Ollie Palmer make their full debuts while Scott Kashket also made his first start in an O’s shirt.
It was the hosts that enjoyed the better of the starts as Orient were reduced to very little possession and Carl Baker tested O’s goalkeeper Alex Cisak early on with a drilled shot from the edge of the box which was parried away.
Orient responded with an effort of their own immediately after however as Dean Cox floated a free-kick into the penalty area that Mathieu Baudry could only send direct over the bar.
Having witnessed his side be on the back foot for the opening ten minutes O’s Head Coach Ian Hendon shuffled the formation to a 4-2-3-1 to match the hosts as Scott Kashket took up a deeper role behind Ollie Palmer.
The change in formation appeared to be serving the visitors well and good work from Bradley Pritchard in the middle of the park to regain possession allowed Blair Turgott to drive towards the edge of the penalty area before dragging a shot just wide.
The tie soon settled into a tight affair with neither side managing to create any clear cut chances until seven minutes before half time when Orient benefitted from a slice of luck to take the lead.
Following an attack down the left Cox cut back on to his right foot on the corner of the penalty area before whipping in a cross towards Palmer on the six yard line.
The O’s front man was unable to make any real connection with his header but Dons captain Dean Lewington could only slice his right-footed clearance beyond goalkeeper Cody Cropper who slipped on the line.
MK Dons started the second half strongly and only a couple of minutes after the restart Dale Jennings cut inside from the left and unleashed a rasping drive that Cisak parried away well with Simon Church lurking.
Orient were managing to come forward themselves however and Palmer had an opportunity to double their lead when Kashket managed to touch the ball into his path just inside the box but the striker was unable to keep his shot down.
As the second half wore on the O’s continued to remain organised and disciplined and on the 66th minute they could well have been two ahead.
With the ball deep into the hosts half Cox won the ball back from a throw before squaring the ball to Palmer who then adjusted his feet well before smashing a shot towards the near post, only to see his shot crash back off the frame of the goal and the back of Cropper before eventually being cleared.
Out of the two teams it was Orient who looked more likely to score the next goal and Baudry squandered another chance from a corner when he rose well to meet Cox’s delivery but failed to keep his effort on target.
As the match entered the final ten minutes Orient Head Coach Ian Hendon made a double substitution as he brought on Frazer Shaw and Jay Simpson for Alan Dunne and Palmer who had both put in tireless displays.
Having only been on the pitch for a matter of minutes Simpson then had the chance to settle the tie with five minutes left to play.
The brought the ball down superbly on the halfway line and set the ball into the path of Kashket who drove towards the edge of the Dons area before rolling the squaring the ball back to Simpson who saw his effort parried away for a corner.
The miss was to prove costly though as with one minute of normal time left to play MK Dons equalised through another own goal.
Substitute Ben Reeves sent in a teasing cross from the right and despite Baudry getting to the ball before Church, he could only direct his header into his own net.
Two minutes later the O’s were then dealt an even crueller blow as MK Dons grabbed a winner when the ball was played across to Carl Baker inside the penalty area who then drilled a low shot into the bottom far corner.
MK DONS: Cropper, Hodson, Upson (McFadzean 76), Walsh, Lewington (C), Aguza, Rasulo, Baker, Benavente (Gallagher 76), Jennings (Reeves 67), Church
SUBS: Martin, Spence, Flanagan, Tilney
GOALS: Baudry OG (89), Baker (90+1)
BOOKINGS: Upson (36)
ORIENT: Cisak, Clohessy, Baudry (C), Essam, Dunne (Shaw 81), Turgott, Pritchard, Moore, Cox, Palmer (Simpson 81), Kashket
SUBS: Grainger, Ling, James, Moncur, Adeboyejo
GOALS: Lewington OG (38)
BOOKINGS: Pritchard (65), Baudry (69)
REFEREE: Simon Hooper
ATTENDANCE: 5,444 (390)