Lita, who arrived on loan from Swansea 24 hours earlier, struck with one minute remaining as the struggling Owls completed a remarkable turnaround.
Johnnie Jackson had put Charlton into the lead early in the second half, and Chris Powell's in-form side also rattled the woodwork twice through Michael Morrison and Scott Wagstaff.
But Reda Johnson made up for a horror miss in the first half with the 84th-minute equaliser, and substitute Lita ended Charlton's three-game winning streak in the Championship.
Johnson would have otherwise had nightmares about his howler, after he somehow scooped the ball wide of an open goal from eight yards after Addicks keeper Ben Hamer spilled a high ball.
Wednesday could have taken an earlier lead when Anthony Gardner met debutant Danny Pugh's corner, but his header was kept out by a combination of team-mate Michail Antonio's backside and Hamer.
Dale Stephens swung in a deep free-kick which Matt Taylor nodded back across goal and former Owls centre-half Morrison headed against the crossbar.
But Charlton did not have to wait long after the break to take the lead.
One minute into the second half full-back Chris Solly charged down the right and crossed to the far post.
Bradley Pritchard did well to control the high ball and lay it back for fellow midfielder Jackson to prod home from eight yards.
Wednesday promptly threw on Lita and the former Addicks striker forced Hamer to make a fine save with a low, curling 25-yard drive.
Charlton could have made the game safe in the 67th minute when Wagstaff drove goalwards from the edge of the area but his effort cannoned back off the near post to safety.
Instead, Wednesday drew level when defender Johnson rose highest at the far post and planted a superb looping header over Hamer and into the net.
And with time running out Lita stunned The Valley when he swept in Jermaine Johnson's cross to snatch a memorable win.