Wednesday's good run of results in October came to an end at The Valley as a first half goal from Scott Wagstaff gave the Addicks a 1-0 victory.
The hosts largely controlled the first half although Wednesday upped the ante after the break but they couldn't find a way past a stern Charlton side who held on for three points.
Wednesday made three changes in the capital with Neil Mellor, Gary Teale and Tommy Spurr all starting against Charlton.
Nicky Weaver took the captain's armband in the absence of Darren Purse, who was ruled out through suspension.
With the Owls forced into changes at the back, Spurr and Mark Beevers lined up in central defence with Daniel Jones at left back and Lewis Buxton right back.
And the Wednesday backline had to hold strong in the opening few minutes but had Weaver to thank for making a superb save from Matt Fry.
Following a flurry of corners for the home side, the Charlton left back struck first time from outside the area and Weaver had to watch the swerving effort all the way but was equal to the strike.
Johnnie Jackson was next to force a smart save from Weaver when the midfielder cut in from the left but his low daisycutter was pushed away by the Owls' number one as the Addicks pressed for an early goal.
Marcus Tudgay then came close for the visitors when the striker latched onto Tommy Miller's long ball forward and did well to force Rob Elliot into making a save at his near post.
But Charlton remained in the ascendancy, keeping Wednesday on the back foot and were first to strike at The Valley through Wagstaff.
The ball fell to the youngster outside the 18-yard-box and, after seeing his first shot closed down by Giles Coke, thumped the ball into the bottom corner at the second bite of the cherry.
On the half-hour mark, Weaver was again to thank for keeping the Addicks at bay.
Wagstaff was looking a threat in the final third and, after a smart turn, curled his effort on target but Weaver was on hand to tip over the bar.
But moments later Wednesday had a good chance to level as Buxton fizzed a low ball across the face of goal but both Tudgay and Mellor saw their efforts blocked out six yards from goal, with appeals for handball turned away by the referee.
Mellor almost fired the Owls level moments before the interval as Addicks keeper Elliot miskicked his clearance and the on-loan striker was quick to pounce but blasted inches wide from 20 yards.
Minutes after the restart and the Owls had another half shout for a penalty when Therry Racon bundled Mellor over yards from goal but nothing given in what was shaping up to be an open second half.
The Owls hit Charlton with a swift counter attack that saw Coke burst forward down the left who tried to find Teale in the box but Elliot managed to scramble the ball to safety.
That was Teale's last action as the winger was replaced by Jermaine Johnson on the hour mark.
Johnson looked lively after his introduction and was out to take the game to Charlton as the visitors began to gain some momentum.
Wednesday were without doubt an improved side in the second half but it was Charlton who had a golden chance to effectively kill the game when Lee Martin showed good quality down the left and delivered a dangerous ball into Paul Benson who prodded over the bar.
Eight minutes from time and Johnson was causing trouble for the Addicks again and after beating his marker on the right, the Jamaican whipped in a decent cross that Mellor could only head wide.
Four minutes of added time was indicated by the fourth official but 1-0 was how it finished in South East London.
Charlton: Elliot, Fancis, Jackson, Semedo, Wagstaff, Racon, Doherty, Benson, Fry, Anyinsah (Martin 71), Dailly,
Unused substitutes: Worner, Llera, Abbott, Martin, Sodje, McCormack, Fortune
Owls: Weaver, Spurr, Buxton, Beevers, Jones, Coke, Potter, Miller, Teale (Johnson 59), Mellor, Tudgay (Morrison 68)
Unused substitutes: Jameson, Hinds, O'Connor, Sedgwick, Heffernan