Guy Luzon had secured the first win of his reign with a crushing 3-0 win at troubled Brentford last time out and followed that up with another impressive performance.
Frederic Bulot smashed the visitors in front at the DW Stadium before turning provider for Igor Vetokele in the second of nine added minutes in the first half after Leon Clarke suffered a nasty-looking head injury.
Chris Eagles grabbed a debut goal two minutes from the end to put daylight between Charlton and the bottom three, while keeping Wigan marooned firmly within it.
In League Two, Cheltenham Town marked their first game since Russell Milton's appointment to the end of the season with a 1-1 draw at Accrington Stanley.
Wes Burns fired Cheltenham into a half-time lead, but they could not secure a first win in eight games as Shay McCartan snatched a share of the spoils.
