Hosts claim the three points
Goals from Jayden Stockley and Alex Gilbey condemned Town to defeat at The Valley.
Interim manager John McGreal made five changes to the side who drew with Barrow in the FA Cup on Saturday.
George Edmundson, Kane Vincent-Young, Lee Evans, Sone Aluko and Kyle Edwards all returned to the side.
Charlton won a couple of free-kicks in good positions inside the opening 15 minutes, the latter being headed wide of the mark by Jason Pearce at the back post.
The hosts took the lead on 27 minutes. Christian Walton made a strong initial save from Conor Washington after he had got in behind the defence but Stockley was in the right place to drill into the back of the net from eight yards.
Washington looked set to get one-on-one with Walton again but Edmundson recovered well to throw his body in the way of the striker's low drive.
Town's best two chances of the half came just before the break. First, the midfielder headed over from a Scott Fraser corner before, a few moments later, he saw an effort from 25 yards deflected just wide.
The Blues had Walton to thank for keeping the deficit at just one goal shortly after the restart, the 'keeper saving Ben Purrington's header at point-blank range after a cross had deflected to him at the back post.
Elliot Lee headed over the crossbar from six yards a few minutes later, with Toto Nsiala nodding narrowly wide following an Evans free-kick as the clock hit an hour played.
Nsiala denied the hosts a second at the other end 10 minutes later, blocking Gilbey's close-range effort.
Walton continued his impressive outing between the goalposts with 12 minutes remaining, turning away Washington's well-struck low shot with his outstretched leg before denying the Addicks' striker again moments later following an improvised effort from 10 yards out.
Gilbey beat a man before slotting into the bottom corner to seal the points for the hosts with two minutes remaining.
Charlton: MacGillivray, Purrington, Dobson, Famewo, Pearce (C), Jaiyesimi (Leko 69'), Stockley, Gilbey, Washington, Lee, Clare.
Subs: Henderson, Kirk, Davison, Watson, Souare, Elerewe.
Town: Walton, Vincent-Young, Nsiala, Edmundson, Donacien, Evans, Morsy (C), Aluko (Chaplin 69'), Fraser (Pigott 64'), Edwards (Humphreys 83'), Bonne.
Subs: Hladky, Burgess, Penney, El Mizouni.
Attendance: 26,376 (3,159 Town fans).