Lita, who arrived on loan from Swansea 24 hours earlier, struck with one minute remaining as the struggling Owls completed a remarkable turnaround.
The Owls had a let-off in the first half after Lewis Buxton went into the book for leaving Scott Wagstaff in a heap out on the right.
From the resulting free-kick Dale Stephens swung in a deep cross which Matt Taylor nodded back across goal and former Owls centre-half Michael Morrison headed against the crossbar.
However, Charlton did grab 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 Johnnie Jackson to prod home from eight yards.
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 Reda Johnson rose highest at the far post and planted a superb looping header over Ben 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.
- Sports & Recreation
- Scott Wagstaff
- Lewis Buxton