Sunderland dominated the possession from start to finish, but strikes from Ben Watson and former Newcastle man Charles N'Zogbia either side of a Grant Leadbitter goal clinched victory for the visitors.
Sunderland will be left to bemoan their lack of invention in the final third, as they enjoyed the lion's share of the ball without causing much concern to Chris Kirkland in the Wigan goal.
More worryingly though, the result will have the Black Cats fans contemplating the possibility of relegation once again as the season draws to its climax.
Wigan on the other hand will be delighted with a fantastic defensive showing and some true individual quality that drove them to a first win in nine Premier League games.
Early openerThe game was only 12 minutes old when the home rearguard backed away from a high ball as it bounced 25 yards out.
Watson, however, needed no second invitation to drill a controlled volley past Marton Fulop for his first goal since completing a £2million January move from Crystal Palace.
Kirkland did have to pull off a fine double save from Andy Reid's deflected effort and Steed Malbranque's follow-up five minutes later as the Wearsiders responded, although he spent much of the opening 45 minutes picking off wayward crosses with little difficulty.
He was finally beaten four minutes before the break when, after Cisse and Jones had helped on Fulop's clearance, Leadbitter stabbed the ball past him.
However, the respite was short-lived as the visitors once again demonstrated their ability to open up their opponents.
With Jones down in the Wigan box after challenging for a high ball, Paul Scharner flicked on for N'Zogbia, who raced from his own half into the box before beating Fulop with a left-foot shot.
Defensive strengthSunderland returned knowing they would have to be much, much better to rescue the game but made little impression in the early stages of the second half.
Boyce had to react smartly with 53 minutes gone to clear Dean Whitehead's near-post cross at the second attempt with Cisse sniffing an opportunity.
However, the game should have effectively been over three minutes later when N'Zogbia played Scharner in on the left only for Fulop to block with his legs.
Sbragia's response was to withdraw wide men Reid and Malbranque and send on Daryl Murphy and Carlos Edwards, but the changes had little effect as the visitors stood firm.
Indeed, they would have increased their lead with 17 minutes remaining had Fulop not dived low to his right to keep out Watson's dipping free-kick.
Leadbitter saw what he thought was a second equaliser rightly ruled out for offside three minutes later, and Sbragia swiftly played his last card when he withdrew defender Tal Ben Haim and sent on a fourth striker, David Healy.
But his side's fortunes were summed up in the dying minutes when Jones lashed a shot wildly off target and Murphy completely missed his kick in front of goal.
1st Half Goals
Shots on Target
Shots off Target