Boss Owen Coyle knew nothing more than a win would ease the pressure swirling around his side after a miserable run of 11 losses in 12 league games stretching back to last season.
Nigel Reo-Coker gave the visitors the start they so badly needed when he prodded home in the fourth minute, then David Ngog netted shortly after Mohamed Diame's superb 40th-minute equaliser.
And after Bolton had failed to wrap it up when Ali Al Habsi saved Kevin Davies' 70th- minute penalty, Eagles made sure by firing home after a mistake by Antolin Alcaraz.
Having started the game bottom of the table, Bolton's win suddenly turned the pressure on Roberto Martinez's Wigan, who have now lost five league games in a row.
Wigan never recovered from a fine start by Bolton, with Coyle's men getting a dream start in the fourth minute when Eagles crossed for Reo-Coker to prod home just ahead of the hapless Alcaraz.
Bolton's storming start continued with Pratley finding room in the box and firing a curling shot which was well saved by former Trotters goalkeeper Al Habsi.
Martinez's men gradually started to claw their way back into the the game, but it was still the visitors who had the clear-cut chances with Ngog coming close.
The home side were having to rely on set-pieces and Ben Watson came close to an unlikely equaliser on the half-hour when his dipping corner almost eluded Jussi Jaaskelainen.
But when Wigan's big chance came it was brilliantly executed by Diame, who unleashed a curling right-foot shot from outside the box which blazed past Jaaskelainen on 40 minutes.
It was a superb riposte by Diame, who had also scored for the Latics against Tottenham in their last home game and was beginning to show plenty of promise.
But Bolton went back in front in first-half injury-time when Davies dispossessed Steve Gohouri and fed Ngog, who shot home low to Al Habsi's right.
Martinez threw on Hugo Rodallega at half-time after a month out with a knee injury but Bolton had the first chance of the second period when Petrov forced a save from Al Habsi.
Emmerson Boyce shot into the side netting from a tight angle before Rodallega blasted his first effort which was blocked at close quarters by Wheater.
Rodallega came close in the 53rd minute when Victor Moses fed him at the second attempt from the right and the striker's bobbling shot was gathered well by Jaaskelainen.
Wigan's forward moves were becoming more urgent, with Moses cutting inside and clattering a low shot off the legs of Paul Robinson before narrowly missing the resulting Boyce corner.
Moses won a dangerous free-kick on the edge of the box in the 67th minute after a foul by Dedryck Boyata, but Rodallega spooned his set-piece over the bar.
Boyata should have made the points certain for Bolton in the 70th minute when he met a Petrov free-kick with a low header at point-blank range but diverted it wide.
And moments later Al Habsi was almost guilty of an horrendous blunder when he spilled a harmless shot from Eagles out for a corner.
From the set-piece Caldwell was judged to have hauled down Boyata, but Al Habsi redeemed himself with a brilliant save from Davies, and Boyata blazed the rebound over.
But Bolton wrapped up victory in injury time when Eagles seized on a mistake by Alcaraz to cut inside the Wigan box and drill a low shot past Al Habsi.