Town had enough chances to have left the DW Stadium with all three points but goals from Ryan Shotton and Nick Powell gave Wigan the win.
Latics’ ‘keeper Scott Carson was the outstanding player on the pitch, making a series of fine saves including a brilliant block to keep out Daryl Murphy’s left foot effort.
Shotton was left alone to head the home side in front early on though and Dean Gerken was caught out for the second on 90 minutes, losing the ball to Powell inside the box as the Latics took the points despite being second best for much of the game.
Town boss Mick McCarthy made one change to the side that beat Yeovil, Paul Anderson having recovered from a groin injury and replacing Carlos Edwards in midfield.
Blues could have been ahead inside the first minute, Anderson’s corner headed downwards and hitting the underside of the bar, then Cole Skuse almost made Carson pay for not gathering the ball as the ‘keeper slid out to clear the danger.
Wigan had an anxious wait after referee James Adcock spoke to Jean Beausejour following a clash with Christophe Berra but on 12 minutes, the Latics were ahead – Shotton heading in at the far post.
Carson was quick off his line as Anderson threatened, the ‘keeper then turning provider with a superb kick-out that saw James McClean weave his way past two defenders in the box. A great challenge from Luke Hyam robbed the Latic as he prepared to shoot.
Town matched the FA Cup holders blow for blow and it needed a timely challenge from James McArthur to prevent David McGoldrick getting in, the Town striker then heading over.
Ryan Tunnicliffe was denied by Thomas Rogne’s challenge, the defender blocking Murphy’s follow-up strike as Blues pressed for an equaliser.
Anderson leapt well but couldn’t keep his header down, the winger looking lively and it was from his cross that McGoldrick was inches away from an equaliser with a glancing header.
Blues had a gilt-edged chance to level the scores the play deserved but Carson beat out Murphy’s close range strike, the ‘keeper having more time to parry Cole Skuse’s 30 yarder.
Berra picked up the first booking of the game for a foul on McClean, Callum McManaman sending a left foot shot over in the last effort of a first-half that should have seen Town go into the break at least level and really in front.
Town began the second-half on the front foot, Carson – the far busier of the two ‘keepers – gathering at his near post from Tunnicliffe’s cross, the Manchester United loanee bringing another save from the England international with a drive from the edge of the box.
Tommy Smith joined Berra in the book for foul on McManaman and from the resultant free-kick Wigan should have added a second, Rogne heading wide from six yards out.
Blues made a first change on the hour, Paul Taylor replacing Anderson, the substitute firing over from the angle of the box with his first touch.
McManaman dragged his shot wide in his last touch of the game, the striker limping off to be replaced by Roger Espinoza midway through the second-half.
McClean had a goalbound shot headed out by Smith, while at the other end Shotton did well to deny Taylor as he burst into the box.
Frank Nouble replaced Murphy for the last 15 minutes in Town’s second change, Emmerson Boyce on for James Perch in a swap for Owen Coyle’s side.
Nick Powell’s diving header from Ben Watson went just wide, McArthur then failing to take advantage from inside the Town box after the ball broke to him off Berra.
Town had another great chance on 83 minutes but Watson threw himself in the way of McGoldrick’s effort from six yards and the Latics scrambled the ball away.
Blues made a final change with Anthony Wordsworth on for Hyam, Wigan following suit with Chris McCann on for Beausejour.
The outstanding Carson threw himself to his right to keep out a Berra piledriver, the former West Brom ‘keeper plucking Wordsworth’s header out of the air and seconds later the game was sealed when Powell capitalised on in-decision by Gerken and kept his composure to score from three yards.