The Molineux side finished the campaign having conceded 82 goals and it was their leaky defence which saw them concede an early lead at the DW Stadium.
Even a late consolation to improve the scoreline could not gloss over their problems and new manager Stale Solbakken will have much to address over the summer.
Wigan capitalised on some weak defending as Emmerson Boyce, who has excelled on the right of midfield since manager Roberto Martinez adopted a 3-4-3 formation, scored twice and could easily have had a hat-trick.
Matt Jarvis had put Wolves ahead but Franco Di Santo and Boyce turned things around very quickly and when the latter spectacularly volleyed home in the second half the result was put beyond Wolves despite substitute Steven Fletcher's late consolation.
The first-half action was encapsulated in a manic six minutes which perfectly summed up Wolves' dreadfully disappointing season and highlighted why Wigan survived against the odds.
In the ninth minute Stephen Ward played in Jarvis down the left but when he collected the ball out wide he still had plenty to do. But having cut inside on to his right foot he curled a perfectly-weighted shot around Gary Caldwell, Wigan's player of the season, and past goalkeeper Ali Al Habsi into the far corner of the net.
The joy of the self-deprecating Wolves fans, who frequently sang about going to Barnsley next season, was short-lived, however, as Wigan were level soon after.
Stephen Hunt dawdled in possession 30 yards out and James McCarthy required no second invitation to nick the ball off him. Even though he eventually ran into traffic on the edge of the penalty area Di Santo was on hand to fire home a low shot.
Wolves' lackadaisical attitude to defending cost them again barely three minutes later when Jean Beausejour flicked over a corner from the left and Boyce headed in from 12 yards.
The visiting fans had clearly decided they were determined to enjoy themselves with the Championship lying in wait next season and celebrated the goal with possibly more vigour than they had when Jarvis had put them in front.
Early in the second half goalkeeper Dorus de Vries had to be replaced by Carl Ikeme, who a month ago was playing at Doncaster before being recalled after injury to Wayne Hennessey and Rovers' relegation to League One.
With 45 minutes to end their top-flight stay on a high, Wolves had the first chance of the second half when Kevin Doyle's header was well saved by Al Habsi at the foot of the far post.
But Wigan responded with two good attempts of their own with Shaun Maloney's shot saved by Ikeme after a through-ball from substitute Albert Crusat, who also drove a shot into the side-netting having been put through by Di Santo.
Hugo Rodallega, whose contract is up next month, came on for what was more than likely his farewell appearance and immediately set up the third. His header down dropped right into Boyce's path and he smashed a swerving volley into the top corner from 20 yards.
With six minutes remaining Boyce had a chance to shoot for his hat-trick but sentimentality - or a defender's instinct - took over and he squared for Rodallega but the ball was hacked clear before it reached the Colombia international.
A mistake by Adrian Lopez allowed Doyle to dispossess him on the edge of the area and when the ball dropped to substitute Fletcher he knocked in a consolation.
Rodallega almost signed off in fairytale fashion by hitting the post seconds from the final whistle, which brought a sea of fans flooding on to the pitch to celebrate securing an eighth successive season in the top flight.