Dwight Tiendalli's scrappy winner completed a stunning turnaround to earn Swansea its first win in seven games and push Wigan closer to relegation.
Roger Espinoza put the Latics ahead with an excellent volley on the stroke of halftime, but was outdone by Angel Rangel just after the break as he equalized for Swansea. James McCarthy's gave the Roberto Martinez's troops hope of securing a crucial victory by restoring the home side's lead with a composed finish.
But a spirited comeback from Michael Laudrup's men saw Itay Shechter's looped effort restore parity before a suicidal defensive mistake allowed Tiendalli to stab home to crucial goal and leave the Latics with a mountain to climb if they're to achieve Premier League safety in their final two fixtures.
Roberto Martinez made three changes to the side that beat West Brom on Saturday, with Roger Espinoza replacing the injured Jean Beausejour, while captain Gary Caldwell and James McArhur came in at the expense of Ronnie Stam and Jordi Gomez.
Laudrup also decided to tinker with the Swansea lineup, handing a rare start to captain Gary Monk, while Dwight Tiendalli and Itay Schechter also came in, with Chico Flores and Nathan Dyer dropping out alongside top scorer Michu, who wasn’t even on the bench.
After results across the weekend dropped nicely for them Martinez knew a win against his former employers in this much fabled game-in-hand would see Wigan leapfrog Newcastle and Norwich out of the bottom three on goal difference. Defeat, on the other hand, was unthinkable.
However, they almost fell behind in the third minute when Wayne Routledge caught Espinoza on his heels, but could only fire into the side netting when through on goal.
The home side eventually settled into their usual passing rhythm and went close to equalizing when Arouna Kone unleashed a 25-yard drive that Michel Vorm was equal to in the Swansea goal.
Ashley Williams then scooped an indirect free-kick over the bar from eight-yards, after Joel Robles had picked up Caldwell’s nervous backpass in Swansea’s best chance of the half.
It proved a pivotal miss as Wigan deservedly broke the deadlock on the stroke of half time as Espinoza, showed superb technique to squeeze a first-time volley in at the near post from Vorm’s miscued punch.
But any momentum gained from taking the lead wasn’t carried over across the interval and Swansea within four minutes. Routledge’s elegant lofted pass picked out Rangel, who’s controlled volley across goal, clipped the far post before going in.
But Wigan’s recent revival has been underpinned by a mean fighting spirit and it equalized almost immediately as Caldwell’s pass split the visiting defense to find McCarthy and the midfielder finished past Vorm.
Shooting itself in the foot is another of its quirks, and just moments after James McArthur squandered a golden opportunity to make it 3-1 they were pegged back once again when Shechter, anonymous for much of the hour played, saw his snap shot deflect past the despairing glove of Robles.
With a point not good enough to shift them to a position of safety Wigan upped the ante and were only prevented from taking the lead for a third time by Vorm’s stunning point-blank save to keep out Caldwell’s bullet header.
And the consequences were duly felt with 15 minutes remaining as a catastrophic mix up in the six-yard area allowed Tiendalli to sneak in unannounced and poke the ball home to put Swansea in front for the first time.
A sickening clash between Vorm and teammate Ben Davies saw the Swansea goalkeeper stretchered off after lengthy treatment that offered Wigan the opportunity to regroup.
Bur even with nine minutes of added on time afforded to salvage a point they came up short, with Kone twice thwarted by Vorm in the closing stages.