Beaten only once on their travels this season, Martin O'Neill's team had to dig deep with Wigan good value for their first-half lead provided by Titus Bramble.
But once Curtis Davies had levelled it up, they refused to settle for a point and finally clinched all three courtesy of leading scorer Gabriel Agbonlahor.
Villa had suffered an early blow at a rain-swept JJB Stadium when striker John Carew had to quit the action after only ten minutes when he was injured in a collision with Paul Scharner.
Wigan carved out the first half chance of the game when Ryan Taylor's free-kick fell to the feet of Marcus Bent six yards out, but he failed to control it and the ball rolled safely to Scott Carson.
Bent then turned provider with a good cross from the right, but Antoine Sibierski snatched at it and the shot went wide.
There was anxiety for Wigan when Scharner gave the ball away with a poor pass to let Agbonlahor in, but the Austria defender reacted well to get back and atone for the mistake.
The Latics threatened again when Taylor had a shot deflected by Olof Mellberg and from the corner they grabbed the lead.
Taylor, compared to David Beckham by manager Steve Bruce for his deadball quality, fired in a beauty and Bramble won the aerial battle with Martin Laursen to head in from six yards to register his first goal for the club.
With skipper Gareth Barry more involved, Villa went chasing an equaliser with Shaun Maloney forcing Chris Kirkland into action with a powerful long-range effort and Ashley Young blazed one across goal.
Wigan had another chance but Sibierski slipped as he went to shoot and at the other end, Maloney failed to cash in on a free-kick after hammering it over the bar.
But Villa levelled it up with a carbon copy of the Wigan goal.
Barry's delivery from the corner was top class and Davies headed in the equaliser on his first league start.
Villa inflicted more suffering when Young got away from Mario Melchiot, crossed from the byline and Agbonlahor took advantage of hesitancy from Bramble and Kirkland to glance home the winner.