The hosts were second best for much of the first half and Blackburn deservedly took the lead through Jason Roberts only for James McCarthy to draw Wigan level 10 minutes before half-time.
The game really got going in the second half as Hugo Rodallega and McCarthy put Latics two goals ahead before Christopher Samba pulled one back. Ben Watson and David Dunn then netted a penalty apiece as Wigan held on for a priceless victory.
Wigan welcomed back captain Antolin Alcaraz after three weeks out injured and Victor Moses was also handed a rare start, while Blackburn included Brett Emerton after he returned from Asian Cup duty with Australia.
Rovers have looked a decent outfit under Steve Kean and were hoping to get back to winning ways after successive defeats at the hands of Aston Villa and Tottenham.
And it was certainly the visitors who provided most of the attacking threat in the early stages as Ali Al Habsi was forced to repel a barrage of balls fired into his box.
The Latics keeper also did well to keep out a fierce free-kick from Morten Gamst Pedersen, while Wigan relied mostly on set-pieces and counter-attacks.
So it was no surprise when Rovers took the lead in the 23rd minute through former Latics striker Roberts.
A lovely ball from Junior Hoilett found Emerton in acres of space down the right and he took the ball to the byline before pulling it back for Roberts, who could not miss from three yards.
Rovers continued to press and Benjani Mwaruwari should have done better with a header in front of goal from another terrific delivery by Pedersen, but in the 35th minute Wigan shocked their opponents by drawing level.
Victor Moses did brilliantly to jink into the box and set up Emmerson Boyce for a shot that was saved by Paul Robinson, but the rebound fell for McCarthy, who tucked the ball away from a tight angle.
The pitch was cutting up very badly in the rain, but that did not stop Rodallega giving Wigan the lead less than five minutes into the second half.
Moses' flick-on from Al Habsi's goal-kick caught out Samba, allowing Rodallega a run on goal, and the Colombian neatly sidestepped Robinson before slotting in a precise finish.
There was no doubt which team was on top now and six minutes later Wigan netted their third courtesy of some brilliant skill by McCarthy.
Charles N'Zogbia was central to the goal, the midfielder first seeing a shot well saved by Robinson and then picking up the rebound. N'Zogbia eventually played in McCarthy, who juggled the ball from right to left foot before guiding a shot just inside the far post.
Just when Wigan seemed to have taken a stranglehold on the game, though, Blackburn pulled one back, and it could not have been simpler as Pedersen's corner picked out the head of the towering Samba.
The defender's goal came less than two minutes after McCarthy's strike, but incredibly they found themselves facing a two-goal deficit again in the 65th minute.
Rovers' complaints were understandable as Michel Salgado was adjudged to have tripped Mohamed Diame just inside the area, but Watson exploited the situation fully by sending Robinson the wrong way from the penalty spot.
Two minutes later Tom Cleverley replaced Moses for his first appearance after a month out injured, with Blackburn bringing on Mame Biram Diouf and David Dunn.
Diouf had a decent opportunity to reduce Rovers' arrears when he found space on the right of the area but he was closed down quickly by a mass of Wigan defenders and could only shoot wide.
Blackburn did manage a third in the 81st minute, though, and again it came from the penalty spot. Boyce lunged in recklessly on Dunn and the substitute picked himself up to slot the spot-kick beyond the outstretched arm of Al Habsi.
Rovers pushed hard for an equaliser through five minutes of injury time but this time Wigan stood firm to hold onto the three points that lifted them out of the relegation zone.