Morten Gamst Pedersen's corner was headed home by Benni McCarthy on the stroke of half-time and the South African striker set up Ryan Nelsen for his first Rovers goal 15 minutes into the second half.
The victory and a crucial clean sheet was ensured courtesy of some inspired saves from Paul Robinson throughout.
Before the game, Rovers made two changes to the side that lost 1-0 away to Stoke, with midfield duo Tugay and Vince Grella replacing Aaron Mokoena and Keith Andrews, while Chris Samba was again asked to operate in attack.
The visitors also made two changes from their last outing, welcoming back Charles N'Zogbia from a knee injury and captain Lee Cattermole from a four-match ban.
Antonio Valencia had tormented Stephen Warnock in Wigan's 3-0 victory at the JJB Stadium earlier in the season and the Ecuadorian was at it again after just three minutes, getting the better of the left-back on the edge of the box, before seeing his crisp strike bounce back off the underside of the bar.
The early attack acted as a wake-up call for the home side, who stamped their authority on the proceedings from then on.
On 11 minutes, Pedersen's teasing cross was almost forced home by Samba at full stretch, but Titus Bramble just got back to make the block.
From the resulting corner, Chris Kirkland produced a smart stop to keep out McCarthy's header at the far post, before Pedersen dragged an effort wide as Rovers piled on the pressure.
On 24 minutes, Pedersen's long throw found El-Hadji Diouf at the far post, but his header was eventually cleared off the line by Cattermole. At the other end, Valencia's cross was laid off by Hugo Rodallega to Ben Watson in space, but the midfield man sliced his shot high over the bar.
On 39 minutes, Rodallega was unfortunate not to open the scoring with a header but McCarthy did break the deadlock with one of his own on the stroke of half-time.
Pedersen swung in a corner, Kirkland missed his punch and the South African striker headed home into the unguarded net.
Wigan's keeper was again found wanting ten minutes into the second half but, on this occasion, Samba's towering header from Andre Ooijer's cross bounced agonisingly wide of the post.
Less than 60 seconds later, Valencia slipped in Watson, whose low drive was well kept out by Robinson.
The comfort of a second goal was always going to be important for the home side and it duly arrived on the hour mark. After a foul by Paul Scharner on Samba, McCarthy whipped in the free-kick and Nelsen got in front of his marker to glance the ball home.
Wigan were still looking a threat and it took a triple Robinson save to keep them at bay.
On 65 minutes, Valencia's cross found the unmarked N'Zogbia at the far post, but his header was tipped over the bar. From the resulting corner, Robinson produced a brilliant reaction save to deny Emmerson Boyce, before keeping out Valencia's rocket on the follow-up.
The England international then got down well to deny Rodallega and stood up strong to substitute Daniel de Ridder, as Rovers moved six points clear of the bottom three.