The home side gave a first start to £2million pound signing David Cotterill, while Lee McCulloch kept his place in the absence of the injured Emile Heskey.
Charlton boss Iain Dowie kept striker Jimmy Floyd Hasselbaink on the bench despite his two-goal Carling Cup showing at Chesterfield in midweek.
It was the youngster Cotterill who created the first opening for the home side with a run down the right which Charlton keeper Scott Carson collected and was flattened by McCulloch in the process.
If that was one escape for Charlton they were even luckier to survive a ninth minute corner that was whipped in by Kevin Kilbane and took a deflection off the head of defender Talal El Karkouri, only for the ball to be cleared off the line.
But Wigan were not to be denied and four minutes later they took a deserved lead when a long clearance from Chris Kirkland deceived Souleymane Diawara and allowed the chasing McCulloch to blast home.
It was the Scotsman's third goal of the season and just reward for Wigan's early enterprise, but Charlton hit back almost immediately and it needed a timely tackle from Andy Webster to deny Darren Bent a shooting chance.
Bent was again the danger when he burst down the right-hand side and squared the ball back for Jerome Thomas, but his shot flew high into the stands.
Eight minutes later Wigan keeper Kirkland saved from Bent following a Thomas free-kick and from the clearance, which was flicked on by McCulloch, Henri Camara cracked home a superb volley 20 yards, a fitting way to celebrate the birth of a baby son 24 hours earlier.
Dowie replaced Matt Holland with Hasselbaink at half-time in a bid for more firepower and he was quickly in action, his jinking run halted by an Arjan De Zeeuw foul, only for Andy Reid to curl the resulting free-kick high and wide.
But moments later Charlton clawed their way back into the match when Bent took advantage of a slip by Wigan defender Andy Webster and raced through before clipping the ball past Kirkland.
Hasselbaink had a great chance to equalise after 53 minutes when he took advantage of a slip by Leighton Baines, but saw Kirkland produce a great save.
Wigan substitute Matt Jackson then put the game beyond doubt with a great header from Kevin Kilbane's free-kick after 78 minutes.
Charlton substitute Marcus Bent's injury-time strike was scant consolation for the visitors who remain deep in trouble at the wrong end of the table.