In interim boss Graham Barrow's first game in charge, Omar Bogle should have put the Latics in front when he fired wide after rounding Sam Johnstone.
James Chester headed past Matt Gilks to give Villa the lead after the break.
Scott Hogan then nodded in from Albert Adomah's cross, his first goal for Villa since joining from Brentford.
Wigan, who dismissed manager Warren Joyce five days ago, should have taken the lead early on when Bogle hit the side netting from a tight angle.
Both the former Grimsby striker and Gabriel Obertan then fired wide as the hosts had the better of the first half.
Villa had gone close through Chester, who headed inches over just before the break, and it was the Welshman who broke the deadlock when he nodded home from close range with 17 minutes to go.
Johnstone then denied Bogle with his fingertips before Adomah's cross found Hogan, who headed in from close range.
Villa's form has dramatically improved in recent weeks but despite closing the gap on sixth-placed Sheffield Wednesday from 17 to 11 points in their last two games, with just eight games to go a play-off spot for Steve Bruce's 12th-placed side remains unlikely.
Wigan interim manager Graham Barrow:
"There was a satisfaction about the game for so long. Then it was the old sucker punch and we only have ourselves to blame, for the first goal especially.
"Why we switched off so much, I don't know. But I was encouraged by the fact we did work their goalkeeper, probably more than we've worked any goalkeeper.
"There was a lot to be encouraged by across the board. I've asked a lot from the players this week and they've almost produced, but not quite enough."
Aston Villa manager Steve Bruce:
"They gave us a really tough game, that's how difficult the Championship is.
"It's good to see us show a little bit of resilience. But, if we're being honest, we've got to be better than what we've been today.
"At least we stuck at it and we got a win, and that's what this league is all about."
Match ends, Wigan Athletic 0, Aston Villa 2.
Second Half ends, Wigan Athletic 0, Aston Villa 2.
Corner,  Wigan Athletic. Conceded by Mile Jedinak.
Attempt missed. Jordan Amavi (Aston Villa) right footed shot from outside the box misses to the left. Assisted by Scott Hogan with a headed pass.
Foul by Michael Jacobs (Wigan Athletic).
Alan Hutton (Aston Villa) wins a free kick in the defensive half.
Substitution, Aston Villa. Tommy Elphick replaces Albert Adomah.
Goal!  Wigan Athletic 0, Aston Villa 2. Scott Hogan (Aston Villa) header from the centre of the box to the bottom right corner. Assisted by Albert Adomah with a cross.
Substitution, Wigan Athletic. Alex Gilbey replaces Sam Morsy.
Shaun MacDonald (Wigan Athletic) wins a free kick in the defensive half.
Foul by Albert Adomah (Aston Villa).
Corner,  Wigan Athletic. Conceded by Jonathan Kodjia.
Attempt saved. Michael Jacobs (Wigan Athletic) right footed shot from outside the box is saved in the centre of the goal. Assisted by Sam Morsy.
Attempt blocked. Shaun MacDonald (Wigan Athletic) left footed shot from outside the box is blocked.
Dan Burn (Wigan Athletic) wins a free kick in the defensive half.
Foul by Scott Hogan (Aston Villa).
Offside, Wigan Athletic. Omar Bogle tries a through ball, but Ryan Colclough is caught offside.
Corner,  Wigan Athletic. Conceded by Sam Johnstone.
Attempt saved. Omar Bogle (Wigan Athletic) left footed shot from the left side of the box is saved in the bottom right corner. Assisted by Michael Jacobs.
Henri Lansbury (Aston Villa) is shown the yellow card for a bad foul.
Michael Jacobs (Wigan Athletic) wins a free kick in the defensive half.
Foul by Henri Lansbury (Aston Villa).
Goal!  Wigan Athletic 0, Aston Villa 1. James Chester (Aston Villa) header from the centre of the box to the bottom left corner following a corner.
Corner,  Aston Villa. Conceded by Dan Burn.
Foul by Jake Buxton (Wigan Athletic).
Henri Lansbury (Aston Villa) wins a free kick in the defensive half.
Corner,  Wigan Athletic. Conceded by Conor Hourihane.
Attempt blocked. Ryan Colclough (Wigan Athletic) header from the centre of the box is blocked. Assisted by Michael Jacobs with a cross.
Corner,  Wigan Athletic. Conceded by Mile Jedinak.
Attempt blocked. Shaun MacDonald (Wigan Athletic) left footed shot from the right side of the box is blocked.
Sam Morsy (Wigan Athletic) wins a free kick on the right wing.
Foul by Jordan Amavi (Aston Villa).
Attempt missed. Jonathan Kodjia (Aston Villa) right footed shot from outside the box misses to the right. Assisted by Jordan Amavi.
Attempt saved. Ryan Colclough (Wigan Athletic) left footed shot from outside the box is saved in the bottom right corner. Assisted by Callum Connolly.
Offside, Aston Villa. Jonathan Kodjia tries a through ball, but Scott Hogan is caught offside.
Corner,  Aston Villa. Conceded by Jake Buxton.
Corner,  Aston Villa. Conceded by Jamie Hanson.
Foul by Craig Morgan (Wigan Athletic).
Scott Hogan (Aston Villa) wins a free kick in the defensive half.
Corner,  Wigan Athletic. Conceded by Sam Johnstone.
Goals from James Chester and Scott Hogan left managerless Wigan seven points adrift of safety as Aston Villa claimed their fifth win in six games.