Wigan have never lost at Villa Park and a first-half strike from Hugo Rodallega set them on the way to record their fifth game without defeat over Martin O'Neill's team.
Jason Koumas netted a 56th minute second to further boost Wigan, but it could easily have been a more clear-cut victory as only the post and a goal-line clearance prevented other goals.
The defeat is a serious setback for Villa and their suspect defence is in desperate need of shoring up, while the ineffectiveness of Gabby Agbonlahor and Emile Heskey up front is cause for concern.
Wigan's impressive win, carved out by some smart play from Rodellega and Hendry Thomas, only confirmed just how much Villa are going to miss the commanding presence of the departed Martin Laursen and Gareth Barry.
Wigan have invariably done well at Villa Park and under new manager, Roberto Martinez, their latest visit lived up to expectations.
At an early stage Villa made it obvious that much of their attacking play would be from the left as they provided an almost non-stop service for Ashley Young but the tactic mis-fired.
Agbonlahor and Heskey both failed to make contact with one Young cross, while Charles N'Zogbia saw his low shot pushed onto the post by veteran Brad Friedel.
Boosted by his midweek England performance, James Milner played with every confidence and had one shot brilliantly saved by Chris Kirkland from a pass set up by Young.
A few minutes later it was Milner who cleared a Rodellega shot off the line with Friedel well beaten.
The roving Wigan striker could not be denied and in the 31st minute he shook Villa Park with a long-range looping shot from the right into the far corner of the net for only his fourth goal for the north-west club.
Two minutes before the break the Colombian striker was only denied a second goal by Friedel pushing out a leg to save his shot as Villa's suspect defence again displayed their short-comings.
The writing was on the wall for Villa when Koumas collected a low, angled pass and then put the ball through Friedel's legs for Wigan's second goal.
Villa introduced teenager Fabian Delph but the former Leeds player was out of his depth in the circumstances and was replaced by Steve Sidwell as Wigan coasted home.