Sam Baldock missed a late minute penalty as Orient just clinched victory.
Dean Morgan cancelled out Luke Chadwick's opener with captain Stephen Purches hitting a superb second-half winner.
It was a first win for caretaker boss Kevin Nugent and the club's first since November 25.
Meanwhile, Roberto Di Matteo's men are yet to win in 2009.
Dons started the game well and took the lead when Aaron Wilbraham played through Chadwick who put Jordan Spence on the floor as he cut inside and fired a curling shot into the top corner.
But instead of the Dons going on from there, they allowed Orient back in the game as they equalised just four minutes later.
Referee Mr David awarded a harsh free-kick by the corner flag as John Melligan tumbled to the ground under pressure from Dean Lewington.
From the resulting Melligan free-kick, Morgan chested down and fired a shot that deflected past Willy Gueret.
It lifted the visitors and they were the better side for the remainder of the half.
Rossi Jarvis made a meal of the first chance after good work from Morgan, who crossed for the striker at the back post only for him to fire against his own arm.
Then in the last minute of the half, Jarvis did much better with a 25-yard free-kick that was tipped over by Gueret.
The Dons needed a quick start in the second half but were dealt a killer blow as Sean O'Hanlon had to hobble off injured.
He was replaced by Daniel Powell as Jude Stirling moved to centre-back and Wright into an unfamiliar right-back role.
The Dons immediately looked more shaky without the influential centre back and with Navarro mainly playing central midfield on his own, they ooked a little spineless.
Orient second goal still came as a slight surprise though as the ball fell perfectly on the edge of the box for Purches, who hit a thunderous right-footed shot into the very bottom corner of the net.
It finally woke the Dons up who went in search of an equaliser.
Chadwick had a decent left-foot shot from the edge of the box that was well held by Jamie Jones.
Johnson then hit a powerful 25-yard shot that was well held by Jones.
The American winger then showed the Dons frustrations as with 15 minutes to go he appeared to hit out at Jason Demetriou after being fouled.
A minute later it looked like those frustrations would be eased but from eight yards Baldock some how headed Lewington's corner wide.
The chances continued to come as Wright cut back for Powell but from eight yards out he completely missed his shot.
It looked like Orient were going to hang on then in the second minute of added on time the crowd erupted as Jarvis handled Jemal Johnson's corner.
Baldock stepped up in front of the Cowshed but his shot was tipped onto the post by Jones.