Darren Bent scored the only goal as Charlton continued their fine start to the season with a dominant performance.
The Addicks saw Chris Powell's header hit the bar but took the lead when Bent nodded in from close range at the near post following Danny Murphy's cross.
Bent then dragged a second opportunity wide when he was clean through on goal.
Wigan failed to force a save from the Charlton keeper and were fortunate to see Arjan DeZeew's last-ditch tackle come off the post.
In the first-ever game between the sides in the league. the visitors were often second best.
Charlton's dominance was such that their fans frustration at being level after half an hour was clearly evident.
But they did not have to wait too much longer for the breakthrough, Bent heading in at the far post from close range after an excellent run from Danny Murphy.
Charlton were increasing the pressure as the visitors found it difficult to create clear-cut opportunities with Jason Roberts playing on his own up front.
To compound their problems, when they did get the ball Paul Jewell's side failed to make the most of the possession.
The lively Jerome Thomas caused Wigan difficulties down the right all afternoon and he, along with Powell and Luke Young, forced the keeper into some fine saves.
Wigan were committed and enthusiastic but failed to create a meaningful chance.
Jewell made a tactical change at the interval, bringing on Steve McMillan for Alan Mahon, but it failed to make any difference to their fortunes.
But the real problem lay in their lack of firepower and there were no strikers on the bench, Jason Roberts on his own up front.
Midfielder Murphy was running the game for the home side and was replaced late on to a deserved ovation by the home crowd.
On the few occasions Wigan got into attacking situations they were wasteful, typified by Ryan Taylor's free-kick.
Charlton finished on a high, forcing Wigan on to the back foot, and DeZeeuw was relieved to see his tackle come off the post to safety.
The invention of Murphy and the pace of Bent were a threat throughout as the Addicks secured their second win in two games.
Charlton manager Alan Curbishley:
"Being near the top of the table means nothing after two games but I'm delighted with our start to the season and the way we are playing.
"It is great that we have won our games against newly-promoted sides after beating Sunderland last week.
"We controlled the game without really finishing them off and were inches away from getting a second more than once."
Wigan boss Paul Jewell:
"We huffed and puffed but we did not make their keeper work even when we got into good situations.
"We know we need to get someone in quickly who will get us a few goals and we will be working hard on that after the next few days.
"After our performance against Chelsea last week this was a disappointing display and we know we must improve."
Charlton: Andersen, Young, Perry, Hreidarsson, Powell, Rommedahl (Johansson 77), Smertin, Kishishev, Murphy (Hughes 85), Thomas (Bartlett 83), Bent.
Subs Not Used: Fortune, Myhre.
Goals: Bent 42
Wigan: Pollitt, Chimbonda, De Zeeuw, Henchoz, Baines, Bullard, Teale (Taylor 63), Johansson, Francis, Mahon (McMillan 45), Roberts.
Subs Not Used: Jackson, Walsh, Wright.
Ref: R Styles (Hampshire).