Darren Bent took advantage of a rare start to put the visitors ahead less then five minutes in but Emmerson Boyce levelled in the 21st minute before an own goal from Nathan Baker just before half-time put the FA Cup winners ahead.
Wigan pushed for a third at the start of the second half but they were pegged back in the 61st minute by Ron Vlaar's brilliant volley, and that was the way it stayed.
For much of the season it looked like this game could be crucial in the relegation battle but Wigan's defeat by Arsenal on Tuesday meant their fate was already decided.
After the high of last weekend's FA Cup triumph, it has been a rollercoaster week for Roberto Martinez's men.
Martinez had called for this match to be a celebration of all the club have achieved in their time in the top flight, and the FA Cup was brought out onto the pitch before kick-off accompanied by soprano Laurie Ashworth singing 'Abide With Me'.
It was a slow start from the hosts, though, and Ali Al Habsi, brought back into the side in place of Joel Robles today, was called into action in the third minute to punch away Joe Bennett's free-kick.
With Christian Benteke suspended, Bent made his first start since January, and it only took the striker five minutes to make his mark.
Paul Scharner played Bent onside and the former England man netted his first Premier League goal in nearly eight months with a shot that went in off a post.
The game was held up while a flare thrown by the Villa fans burnt itself out in Al Habsi's six-yard box, and it was the visitors showing all the spark.
Wigan did not threaten until the 16th minute, when player of the year Shaun Maloney found Arouna Kone, who was denied by a last-ditch tackle from Baker.
Five minutes later the Latics did level things up as Roger Espinoza swung over a cross from the left and Boyce leapt above Bennett to head powerfully past Brad Guzan.
Both sides threatened to break the deadlock but a poor touch from Gabriel Agbonlahor allowed Al Habsi to gather while Kone could not find James McCarthy when Wigan briefly had a three-on-one situation.
Maloney forced Guzan into a decent save from a 20-yard free-kick in the 40th minute, and in stoppage time the hosts went ahead for the first time.
Maloney's corner caused havoc in the Villa defence and, although Ashley Westwood cleared Ben Watson's shot off the line, he directed the ball against Baker, who could not stop it rolling into the net.
Wigan carried the momentum into the second half and might well have increased their lead on a number of occasions.
First, McCarthy's cross just evaded Kone before Watson tested Guzan, then Baker got the faintest of touches to the ball as McCarthy ran through to allow the Villa keeper to slide out.
Boyce scored twice on the final day of last season and the defender was close to a repeat in the 59th minute as he got on the end of an Espinoza cross but his first effort was headed away from in front of the line by Bennett while his second clipped the top of the bar.
Two minutes later Villa made Wigan pay for failing to take their chances as Bennett's long free-kick was pulled down by Vlaar and then volleyed sublimely into the top corner by the centre-back.
James McArthur thought he had scored an even better goal in the 79th minute with a volley from the corner of the area but it crashed against the bar and Kone was unable to turn in the rebound.
Wigan were desperate to sign off with a win, and half the crowd thought they had managed it in injury time but Roman Golobart's chip landed on top of the net.