Two goals by substitute Nick Powell ensured the FA Cup holders progressed to the fourth round despite stubborn resistance from MK Dons.
The League One side had taken an early lead through Luke Chadwick but with 11 minutes of normal time remaining Powell produced a quality finish to take the tie into extra time and then early in the first period of extra time he added a second. Striker Marc Antoine Fortuné then sealed the result for the Latics with ten minutes remaining.
Wigan now face a home tie against Premier League Crystal Palace on Saturday 25 January.
Partly due to a number of defensive injuries, Uwe Rösler was forced into selecting an experimental line up, with two midfielders in a central defensive trio, Ben Watson and Chris McCann joining recognised centre-half Leon Barnett at the back. Stephen Crainey and James Perch were the wing backs and Fraser Fyvie made a rare start in midfield. Marc Antoine Fortuné was joined by James McClean upfront.
MK Dons started the game confidently and quickly started to cause the experimental Wigan back line problems. Daniel Powell was a constant threat and had an early chance but shot tamely at Ali Al Habsi.
James McClean scuffed a shot wide of the Dons goal but the home side were ahead in the 10th minute. A long ball found Ben Reeves who pulled the ball back to former Manchester United player Chadwick, who finished with some aplomb.
Wigan responded with several attempts at the Dons goal with Fyvie and Roger Espinoza going close.
But the Dons always looked dangerous and could have increased their lead if it was not for the agility of Al Habsi. The Omani international keeper pushed Shaun Williams’s free-kick around the post and produced a miraculous left-handed save to Dean Lewington’s goal bound drive.
Wigan were struggling to replicate their recent Championship form under Rösler and were relieved to go into the half time break only one goal behind.
During the second period the home team had further chances through on-loan Aston Villa youngster Samir Carruthers and Reeves fired over the cross-bar, before Williams had a deflected volley crash against the post.
On 60 minutes the Wigan manager made a double substitution that was to swing the tie in their favour. Emmerson Boyce replaced Perch and Nick Powell came on for Fyvie.
Almost immediately the two substitutes combined to set up McClean but from only six yards out the Irish international managed to mis-kick and then fall over and the chance was wasted.
Boyce was posing a threat as a progressive wing back and Powell was showing the kind of skill that can mesmerize defences.
The Latics equaliser came with 11 minutes remaining, when McCann’s excellent near post cross found Powell who produced a high quality right footed finish.
The FA Cup holders looked like they might seal victory in normal time, but they did score in the first minute of extra-time when Powell broke free of the Dons defence and then delicately chipped the ball over Martin.
Karl Robinson’s team continued to play good counter attacking football and create chances but with ten minutes of extra-time remaining Latics sealed their progress to the fourth round when Espinoza fed Fortune, who finished clinically from 10 yards out.