Record signing Henri Camara struck twice in four minutes as Wigan edged a thriller at the JJB Stadium.
It was their third Premiership double of the season and shot the Latics up into eighth position in the table as they finally picked up their first home win of the calendar year.
They led through a superb strike from Jimmy Bullard before the match exploded with goal action in the second half.
Juan Pablo Angel hit the Villa equaliser before Camara rattled in his double with Liam Ridgewell setting up a nail-biting finish with a second for the visitors.
Both sides had been looking to make further progress up the table with Wigan still harbouring hopes of European competition next season.
Boss Paul Jewell was also demanding an improvement in their home form as Wigan's last win at the JJB Stadium was way back on Boxing Day last year.
With central defenders Matt Jackson and Arjan de Zeeuw both crocked in Saturday's defeat at Newcastle, Stephane Henchoz found himself back in favour and partnering Austrian star Paul Scharner at the back.
Midfielder Damien Francis was also back in the starting line up for the first time in four months as Jewell had a shake-up.
Villa, fresh from beating the old enemy Birmingham, were missing Northern Ireland midfielder Steven Davis with a hamstring injury and David O'Leary kept faith with young defenders Ridgewell and Gary Cahill.
In a frantic start Wigan were restricted to speculative attempts which failed to trouble Thomas Sorensen as Francis, Bullard and Reto Ziegler had shots off target.
Villa went close to getting the opener when Angel spread the ball wide to James Milner, who found Gareth Barry 10 yards out.
The skipper fired in the shot on the turn but John Filan did well to keep it out.
But Wigan broke the deadlock after 25 minutes with a Bullard special - his fourth of the season.
Francis was looking for Camara with the cross but it was hooked away by Cahill before the Wigan striker could pounce.
And it dropped perfectly for Bullard to hammer it in from around 25 yards giving the keeper no chance.
Sorensen kept Villa alive with two quick-fire saves from Jason Roberts and Barry appeared fortunate to escape with a caution after catching Pascal Chimbonda with an elbow in the face.
But Villa levelled it when Milan Baros found sub Gabriel Agbonlahor on the left and Angel swept the cross past John Filan.
That sparked Wigan back into action and they were in front again thanks to a stunning finish by Camara after he had given Cahill the slip.
The Senegal international was celebrating again four minutes later bagging his second of the night after a neat one-two with Chimbonda to make it 11 for the season.
Angel was a whisker away from pulling one back with a header after hat-trick hunting Camara almost hit the target again at the other end.
Villa struck again when Ridgewell took advantage of Filan's hesitation to tuck in a deflected cross which came off the head of Francis to make it 3-2.
Wigan's nerves were showing as Villa piled on the pressure and Graham Kavanagh missed a chance to kill the game when he fired over the bar.
It almost proved costly when a shot from Angel bounced awkwardly in front of Filan but to Wigan's relief it went over the bar.
Incredibly, Bullard missed yet another chance to finish it but time finally ran out for Villa.