A late deflected goal by substitute Franck Moussa condemned Latics to an early season defeat by the Addicks.
The home team had taken the lead after only eight minutes with a long-range strike from Jordan Cousins.
Callum McManaman produced an excellent finish to draw Latics level before the interval.
It was Wigan’s first goal at the Valley in the fourth meeting between the clubs in London, but it was not enough as Moussa stunned Wigan in the 93rd minute. His shot from the edge of the area deflected off Rob Kiernan and looped agonizingly over keeper Scott Carson to give Charlton all three points.
The late winner led to an ugly row between Charlton boss Bob Peeters and Uwe Rösler in the technical area after the Belgian had celebrated the goal right in front of Rösler.
Latics had an early setback when in only the eighth minute Cousins collected Johann Gudmundsson’s pass and unleashed a terrific shot from outside the area and into the top corner of the Wigan net.
But it was not long before Latics were level as in the 22nd minute McManaman cut inside the full back and steered his low shot past Charlton keeper Stephen Henderson.
Loanee Emyr Huws fired over the crossbar from distance and Rhoys Wiggins had a shot well saved by Carson.
Neither side took control on the second half and the match was likely to end in stalemate until Moussa’s late deflected effort broke Wigan hearts.
It has been a disappointing start to the season for Latics with a home draw versus Reading, a Capital One Cup exit to League 2 Burton Albion and now defeat to Charlton. The club now face a difficult trip to Cardiff on Tuesday night but Rösler will be determined to get a positive response from his players.