Wigan striker Hugo Rodallega struck the cruellest possible blow to the Clarets' survival hopes when his injury-time header consigned Burnley to another away defeat.
The Clarets still have just one point to show for their efforts on the road this season as their wait for an away win in the league stretched beyond 12 months.
But this was harsh in the extreme as Brian Laws' men were just a whisker away from recording a first clean sheet since October and keeping Wigan in their sights in the battle to avoid the drop.
The Clarets showed beyond doubt that they have not thrown in the towel in their bid to avoid an instant return to the Championship with a magnificent effort which should have yielded them at least a share of the spoils.
Both sides hit the woodwork with Martin Paterson going closest to winning it for a Burnley side that defended for their lives when required and took the fight to the home side at every opportunity.
But not for the first time the Clarets came out on the wrong side of the most slender of margins and they must now look for a morale-lifting derby win over Blackburn Rovers next Sunday to close the gap on the pack above them.
The Clarets started with another re-shuffled line-up as Clarke Carlisle and Dany Fox both missed out with injury to bring Michael Duff and Stephen Jordan back into the fold.
David Nugent is sent flying by Titus Bramble
And with top-scorer Steven Fletcher and play-maker Kevin McDonald fit again and back on duty, Burnley started in positive fashion.
Graham Alexander saw a shot blocked by Titus Bramble and Fletcher drilled an angled shot into the arms of Chris Kirkland in a frenetic opening.
And with just five minutes gone the Clarets almost got the priceless opening goal.
Bramble was again in the way to charge down a shot from Martin Paterson and when the ball dropped loose Wade Elliott looked a certain scorer until Gary Caldwell threw his body in the way to make a crucial interception.
The Clarets looked the far more composed side and Wigan were lucky to escape unpunished after a quarter of an hour as the over-worked Bramble scythed David Nugent as he ran in on goal but remarkably avoided censure.
Knowing the consequences of a defeat for them, Wigan looked jittery.
But they almost settled those nerves on 18 minutes when Caldwell hit the woodwork.
Kevin McDonald battles away in midfield
A needlessly conceded corner gave the younger brother of Burnley's skipper the heading chance which Elliott did well to deflect against the post from his position on sentry duty at the back stick.
With so much at stake, both teams then retreated into their shells for a spell as they were anxious not to make a mistake.
And while the Clarets played some nice stuff up the third final third they were unable to pick out the killer pass or work Kirkland in the Latics' goal.
Wigan fared no better, however, as Duff made a solid return to the centre of the defence as the home side were comfortably kept at arm's length up to the break.
The Clarets then started the second half as they had the first with McDonald and Fletcher opening up the Wigan defence on the break but again the clear-cut chance failed to materialise as Elliott could not pick out anyone with his cross and Paterson shot tamely at Kirkland.
At the other end the dangerous James McCarthy went down in the box but only under his own momentum and when the ball was suddenly transferred up the pitch Nugent was presented with a chance which he wasted with an early shot which went harmlessly wide.
With the temperature rising on and off the pitch, Kirkland then went down clutching his head as if he had been hit by something thrown from an almost sold-out away end.
Chris Kirkland was apparently hit by a coin
That was the end being attacked by the Clarets and Alexander almost gave the visiting fans something to shout about when he curled a shot just wide after a free-kick had been touched his way 20 yards out.
With the game becoming increasingly stretched and frantic Wigan then went close when Jason Scotland fired just wide and from another McCarthy corner Elliott had to again clear off the line from Rodallega's header.
But despite losing the services of Fletcher with a knock, Burnley came again and this time it was the width of the woodwork that denied them a goal.
Nugent and Paterson combined well and when Nugent chipped a pass into the box Paterson struck a superb angled volley which smacked the bar with 20 minutes to go.
Laws then sent on Chris Eagles in place of Paterson to try and force a winner but in fairness to Wigan they went after the three points themselves and Brian Jensen was forced to make two fine saves in the closing minutes, palming away a McCarthy volley and then tipping over a shot from Mohamed Diame at full stretch.
Martin Paterson works his way through the Wigan defence
The Clarets then had to survive a desperate goalmouth scramble before another break-away saw Robbie Blake slip in Nugent for a chance he just couldn't squeeze past Kirkland.
That looked as though that would be it, but three minutes into added time Rodallega broke Burnley hearts when he met a cross from substitute Victor Moses to plant a thumping header past Jensen.
The Columbian's goal means the Clarets have still never won at Wigan - with this their 13th and surely unluckiest attempt.
Wigan: Kirkland, Melchiot, Caldwell, Bramble, Figueroa, Thomas (Moses 74), McCarthy, Scharner (Scotland 34), Diame, Rodallega, Moreno. Subs: Amaya, Gohouri, Gomez, Sinclair.
Burnley: Jensen, Jordan, Duff, Cort, Mears, Alexander, Elliott, McDonald, Paterson (Eagles 82), Nugent, Fletcher (Blake 68). Subs: Eagles, Weaver, Bikey, Thompson, Cork, Edgar.
Referee: Mike Jones
Booked: McDonald 76, Duff 80, Mears 89
Hugo Rodallega heads home Wigan's winner