Ivan Ramis rose unchallenged to head the visitors into a third-minute lead and although Villa rallied either side of the break, quick-fire strikes from Emmerson Boyce and Arouna Kone condemned Paul Lambert's side to a third consecutive humbling defeat.
They have now conceded 15 goals in their last three matches and drop into 17th place in the Premier League, while Wigan leapfrog them into 16th.
The visitors may have had a penalty within two minutes when Matthew Lowton handled a long ball into the box but the argument was deemed irrelevant when from the resulting corner Ramis was given yards of space in which to thunder a close-range header past Brad Guzan.
Roberto Martinez's side might have had the chance to make it 2-0 six minutes later when Shaun Maloney appeared to be felled by Stephen Ireland inside the box but once again referee Kevin Friend waved the claims away.
Wigan continued to dominate both possession and territory as a Villa side evidently bereft of belief left huge gaps all over their defence and midfield.
Maloney had a great chance to score after 21 minutes but drove his 15-yard shot over the bar while unmarked, before Kone wasted two good opportunities with heavy touches.
Villa suddenly came to life and after Christian Benteke had a goal rightly disallowed, Brett Holman struck the bar with a left-foot half-volley from an angle after a Benteke nod-down.
They continued their revival at the start of the second half and Benteke should have done better with a close-range header.
But they succumbed to a sucker-punch as Boyce exchanged passes with Kone on the edge of the box and swept a neat right-footed shot into the bottom corner.
Villa were stunned and hadn't recovered by the time Franco Di Santo picked the ball up in midfield four minutes later and slid Kone through on goal, the Ivorian neatly rounding Guzan before side-footing into an empty net.
To their credit, Villa responded well, kept fighting and created several half-chances, but a comeback never looked a possibility.