Gerard Houllier's side pulled themselves further away from the Premier League relegation zone as they followed up last weekend's uplifting win over Manchester City in impressive fashion.
James McCarthy marked his return from injury by pulling one back as Villa finished in nervy fashion but the visitors hung on to leave Wigan, with just one win in nine, in trouble in the bottom three.
Wigan looked composed and threatening for large spells but manager Roberto Martinez is unable to transform his team's fortunes by spending £24million on one player like Villa appear to have done by signing Darren Bent.
Bent did not add to his debut goal but his arrival appears to have lifted the midlands club, who are now six points above the drop zone.
Villa manager Houllier chose to change the side that overcame City by making three changes and handing debuts to £6million new signing Jean Makoun and 19-year-old defender Nathan Baker.
Wigan left Mohamed Diame, at the centre of controversy this week after remarks about the town of Wigan were taken out of context, on the bench while defenders Gary Caldwell and Antolin Alcaraz were suspended and injured respectively.
Wigan had the first opportunity when Franco Di Santo headed wide from a Charles N'Zogbia cross.
Villa then began to assert themselves and Bent brilliantly controlled a long ball and pulled back inside the makeshift defender Steven Caldwell only to scuff his shot.
Ali Al Habsi then produced two fine point-blank saves in quick succession to deny Stewart Downing and Bent after a pass from Agbonlahor had opened up the defence.
In a lively opening Wigan responded with N'Zogbia setting up Hugo Rodallega but the Colombian's shot was deflected and Brad Friedel parried.
N'Zogbia also went close after a fine run but his shot dipped over.
Bent claimed he had been tripped by Steven Gohouri as he chased a James Collins pass but referee Jon Moss saw nothing untoward.
McCarthy showed brilliant skill on the edge of the area to clip the ball over Collins and set up Rodallega but his shot appeared to be deflected over, even though Moss gave a goalkick.
Maynor Figueroa worried Villa with a run from the left into the area but never had the ball fully under control and Richard Dunne eventually hammered clear.
After the initial burst the game settled as both defences tightened up.
Di Santo did get in another shot from the left as half-time approached but Friedel was not troubled by his curling effort.
Villa upped the tempo for the start of the second half as Young raced into the area from the halfway line and forced Al Habsi to palm over a fierce drive.
The visitors grabbed the lead from the resulting corner in the 49th minute.
Again Al Habsi did well to keep out Carlos Cuellar's firm header but the ball ballooned into the air and Agbonlahor reacted quickest to nod it over the line as it came down.
The game opened up again and N'Zogbia weaved his way into the Villa area only to see his shot blocked.
Villa countered through Bent but Gohouri managed to get in the way and shield the ball for Al Habsi to gather.
Downing then broke into the area but Al Habsi claimed his low cross.
Young doubled Villa's lead from the penalty spot after being brought down clumsily by Hendry Thomas just after the hour.
The Villa captain made no mistake as he sent Al Habsi the wrong way with a powerful strike.
Bent almost grabbed a third as he raced onto an Agbonlahor throughball but Al Habsi rushed out to deny him again.
Wigan did not give up the fight and pulled a goal back 10 minutes from time, although it did require a huge slice of luck.
There seemed little danger as McCarthy lined up a shot from 30 yards but the ball took a huge deflection off Collins and wrong-footed Friedel to end up in the bottom corner.
The Wigan fans thought they had an equaliser to celebrate moments later when Rodallega flashed inches wide from the edge of the area.
Di Santo also headed at Friedel as the Latics put the visitors under late pressure but they could not force the equaliser.