A stunning hat-trick from Dean Ashton brought Crewe their first victory in eight games and dented Wigan's charge towards the Premiership.
Ashton converted two first-half penalties, the second of which resulted in a sending off for Wigan skipper Jason De Vos.
While the home side battled back to level matters before the break, Ashton sealed the points with a stunning last-minute strike.
In an exciting and sometimes controversial encounter Crewe's lively front pairing of Ashton and Steve Jones gave the Wigan defence no end of problems and, after 19 minutes, a foul by Ian Breckin on Ashton resulted in the striker converting his first spot-kick.
Six minutes later De Vos pulled back the lively Steve Jones and while the referee at first waved play-on he changed his mind on the intervention of an assistant, awarded the kick and dismissed the Latics skipper.
Ten-man Wigan then hit back on the half hour when Lee McCulloch fired home from close range and four minutes later the same player drew them level when he headed home Jimmy Bullard's free-kick.
Both sides could have added further goals after the break but, as Crewe made their extra man tell in the closing stages, the Wigan defence was continually stretched.
It was finally breached in the dying seconds when a superb pass from Kenny Lunt sent Ashton away and he beat Filan with a fierce, angled drive.
It was harsh on Wigan but manager Paul Jewell had no complaints with either penalty, commenting: "The first one was a stonewall spot-kick and the second one even more so. I couldn't ask for any more from the players and lets not forget we are still third in the first division." Crewe boss Dario Gradi admitted his side were fortunate to come away with the three points, adding: "It's nice to be on the end of some good fortune like that, but there was nothing lucky about the build up to the goal and Ashton took it superbly well."