Jordi Gomez and Charles N’Zogbia both struck in the closing three minutes as the Premier League side narrowly avoided a shock at the DW Stadium.
Championship outfit Preston had led after Keith Treacy opened the scoring in the 23rd minute and they hit the woodwork twice through Paul Coutts.
Extra-time was the least Preston deserved but Wigan, having lacked sharpness in the first half, showed more dynamism after the break and finished strongly.
N’Zogbia was the key to their recovery, having entered the fray at the start of the second half, and the result will lift manager Roberto Martinez after a poor start to the campaign.
Martinez had made six changes in attempt to kick-start Wigan’s season after collecting just four points in five Premier League games.
Yet Preston, whose plight in the lower division was worse with three points from seven outings, were moments away from inflicting embarrassment.
And for most of the game what atmosphere there was was mostly created by the huge proportion of Preston fans in the 6,987 crowd – a figure which filled just over a quarter of the ground.
Yet while those North End fans had made the short journey down the M6, one member of their club’s hierarchy who failed to make the start was their chairman Maurice Lindsay, a man synonymous with Wigan.
Lindsay, a familiar face at the stadium after roles on the board with Athletic and the town’s rugby league team, was apparently caught up in traffic.
The few inside the stadium saw the game begin in underwhelming fashion with Wigan dominating possession but lacking a cutting edge.
The game was more than 20 minutes old when Franco di Santo, one of Wigan’s better players, created the hosts’ best early opening when he had a shot deflected after a neat turn.
Gomez fired another chance well over while Chris Brown was similarly off target for Preston.
But Preston, having been starved of the ball, grabbed a surprise lead when Treacy struck low from a set-piece after Danny Mayor was fouled by Maynor Figueroa.
Wigan almost replied instantly as Di Santo flicked the ball over from a corner but Preston were clearly buoyed by their strike.
They began to pass with greater confidence and created a glorious chance after 27 minutes as Mayor crossed and Coutts sidefooted against the base of the post.
Wigan responded with Ben Watson shooting wide after playing a neat one-two with Mauro Boselli.
But that was one of few chances Wigan could muster and they left the field to boos from the home fans.
A quick-thinking DJ tried to rally them by playing Bon Jovi’s ‘Keep the Faith’ and Martinez attempted to inject some life into his team by introducing N’Zogbia.
Latics indeed made a positive start as Di Santo combined well with Ronnie Stam before shooting across the face of goal.
The hosts then carved out an even better opportunity as Boselli played Watson in on goal with a backheel but Andy Lonergan produced a fine save to deny the midfielder.
N’Zogbia then worried Preston with a break from deep inside his own half but the move broke down as Watson got the ball trapped under his feet on the edge of the area.
As Wigan became frustrated, Preston showed signs of tiredness and their tackles became heavier.
One from substitute Jon Parkin on Hendry Thomas particularly incensed Martinez on the sidelines but there was no booking.
Paul Parry and David Gray were not so fortunate, however, as they found their way into referee Jon Moss’ notebook for poor challenges.
Preston missed a glorious chance to kill the game off 15 minutes from time after Parkin picked out Coutts with a fine through-ball.
Coutts raced clear on goal and looked to have scored as he delicately clipped the ball over Al Habsi but saw it rebound off the woodwork for a second time.
Preston paid the penalty as Wigan picked themselves up for a late surge and Gomez levelled with a fine solo effort after jinking into the box three minutes from time.
Latics pushed on for the win but Stam had an effort blocked by Lonergan and N’Zogbia shot narrowly wide.
Preston looked to have held on for extra-time but were stung in stoppage-time as N’Zogbia broke from a Preston corner, played a one-two with James McCarthy, and then blasted past Lonergan.