Wednesday failed to make the most of a flying start and were floored by a hat-trick from Charlton’s on-loan Bolton striker, Marvin Sordell - plus their own flawed defending.
Fine goals by Atdhe Nuhiu and Chris Maguire put the Owls 2-0 up by the eighth minute and they could have stretched their lead with dominant football.
But Sordell kept the Addicks in it with a quick reply, equalised just before half-time, and snapped up the winner in the 63rd minute - with sloppy work by Wednesday preceding all three goals.
Stuart Gray was also not helped by having to reshuffle his team, Changes, some before the game, some during it, included Kieran Lee having to play right-back for the second half.
The result and performance came as an Easter anti-climax for Wednesday after their great win at Bourmenouth on Friday.
But for Charlton and their small following it was a marvellous boost in their fight against relegation.
It was Nuhiu’s best goal for the club when he smashed a shot into the bottom corner from 22 yards at Bournemouth, but his third-minute strike yesterday was just as good.
A long ball by Miguel Llera reached him and from a narrow angle on the left of the Leppings Lane box his left-foot volley flew in off the far post, for his fourth goal in three games and eighth of the season.
Maguire matched that five minutes later. Nuhiu could have shot again but fed the Scot, who stumbled, regained his footing and from the left corner of the area whipped a right-foot effort into the far top corner - his 10th goal for the Owls this season
He stripped off his shirt - earning the mandatory booking - to show a T-shirt with the message, RIP Gran.
Charlton punctured the Wednesday mood of satisfaction with an all-too-simple goal in the 10th minute.
Sordell chased a long ball and held off Helan to roll the ball past Chris Kirkland.
Nuhiu stretched to poke a chance wide after being set up by Maguire, and Lee, running in at the near post, somehow side-footed a right-wing cross by Michail Antonio past the post instead of making it 3-1.
Gray’s attacking line-up caused the Addicks problems in this spell - with Nuhiu producing crowd-pleasing work on the ball.
Gray made three changes to the starting-up, among them a move for Helan to left-back at the expense of Joe Mattock, who was on the bench.
As expected the Owls boss gave starts to Liam Palmer, Giles Coke and Leon Best, while Sam Hutchinson and Lewis Buxton were ruled out by suspension and injury respectively.
Ex-Wednesday centre-half Michael Morrison was in the Charlton side but Richard Wood remained on the bench.
The Owls were so much in control in the first 40 minutes that Sordell’s goal was the only sniff that the Addicks had around their box. With a little more care, Wednesday could have made more of the possession that they enjoyed.
Instead of getting more goals, however, they found themselves pegged back by the visitors’s second notable attack of the match, in the 43rd minute.
Antonio gave the ball away, not far inside the Wednesday half, to Callum Harriott, the left winger who scored in his team’s FA Cup win at Hillsborough. Harriott slotted a pass to Sordell and the forward hit Kirkland’s bottom right-hand corner from the edge of the box.
In the 45th minute, Antonio walked slowly off to be replaced by Jermaine Johnson. There had been a hold-up earlier while Antonio received attention for a facial injury.
In first-half stoppage time, Coke was flattened by a ball in the face and there was a long hold-up.
There was a debate at half-time about whether Antonio’s withdrawal was tactical or a result of a problem.
It had to be a fitness issue that saw Liam Palmer staying off at half-time and Lee switching to right-back. Mattock came on at left-back, Helan moved foward to left wing and
Maguire pushed into central midfield.
Charlton striker Simon Church headed the winner in the cup tie between the teams but was an anonymous figure this time and was taken off early in the second half.
Sordell obviously fancied his chances of a hat-trick as he tried ambitiously to beat Kirkland at his near post and failed.
But the striker gratefully accepted the gift of a bad ball by Nuhiu when he did make it 3-2 in the 63rd minute, running through to slot his shot into the bottom corner.
Wednesday had completely lost their way after such a bright start.
Gray sought fresh impetus by replacing the disappointing Best with Caolan Lavery.
Charlton discovered the confidence that comes with a fightback from two down.
They opened Wednesday up with a flowing move before Llera made a fine block to deflect a shot by Jordan Cousins.
Wednesday huffed and puffed and tried to force their way back into the game but did not show enough quality to break Charlton down.
Goals: Nuhiu 3, Maguire 8 (Wednesday); Sordell 10, 43, 63 (Charlton).
OWLS: Kirkland, Palmer 6 (Mattock h-t, 7), Onyewu 7, Llera 7, Helan 6, Antonio 6 (J Johnson 45, 6), Lee 8, Coke 6, Maguire 8, Best 6 (Lavery 67, 6), Nuhiu 7. Subs not used: Martinez, Taylor, Corry, Afobe.
ADDICKS: Hamer 7, Solly 7, Morrison 6, Dervite 7, Fox 6, Jackson 6, Cousins 7, Poyet 7, Harriott 6 (Wilson 80), Sordell 9 (Obika 90+2), Church 5 (Ajdarevic 54, 6). Subs not used: Thuram-Ulien, Ghoochannejhad, Wood, Petrucci.
Referee: Tony Harrington (Cleveland).