Report: Late Heartbreak
Roberto Martinez reacted at the break by sending on Franco Di Santo - and the Italian almost had an instant effect, racing clear into the box before being denied by a wonderful save by Federici.
Gomez again found space two minutes later - drifting late into the box before clipping a looping volley over the bar.
Jason Roberts had developed a habit of scoring against his former club over the years, and the front man almost did so again at the DW Stadium - spinning on the edge of the box before firing inches wide of Al Habsi's goal.
The equaliser was immanent though, and it came from Jordi Gomez just before the hour mark.
The diminuative forward's initial shot was saved by Federici, but Wigan's number 14 was on hand to bundle home from close range to level the scores.
The Latics' tails were now up, as Gomez again was involved after the restart - forcing another smart save from Reading's 'keeper.
As the Royals tried to relieve the pressure Jay Tabb went down in the six-yard box and prompted strong calls for a penalty - all of which were waved away by Howard Webb.
Perhaps that gave the away side impetus, as Robson-Kanu jinked and twisted on the right wing before clipping in an excellent centre to Le Fondre - who's flicked header was fantastically tipped away by Al Habsi.
The home side did have the ball in the net in the 67th minute, but referee Webb had blown for offside a number of seconds before the ball hit the net.
However - it wasn't long until Wigan were in front. Gomez was unsurprisingly the man to score it - firing in a stooping header from an excellent Beausejour cross.
The game was threatening to become stretched in the final twenty minutes; Kone broke down the left, but as he cut inside saw his low effort well deflected wide by Gorkss' challenge.
Di Santo blazed over with fifteen minutes left on the clock, before McAnuff met Le Fondre's neat chest down on the left side of the area - but could only crash a half volley off target.
Garath McCleary replaced Jay Tabb and received a quick thinking free-kick from Leigertwood on the right wing before scampering to the touchline and squaring for Le Fondre - who uncharacteristically rushed his shot and clipped over the bar.
The pressure was coming from the visitors - and so the equaliser itself wasn't a surprise, though the bizzare fashion it came in was.
Hal Robson-Kanu's snap shot was deflected high into the air, and Al Habsi flapped - stumbling over himself as he dropped the ball and watched it agonisingly roll over the line.
Martinez's men weren't going to take that lying down - Gomez came close to a hat-trick, but saw his low drive deflected wide by Morrison.
And it was to be Gomez who won it in dramatic fashion, clipping home after a swift break away to seal his third of the game and all three points for Athletic.