The Addicks managed to thwart the Owls who were hoping to book a Steel City derby date with Sheffield United in the final eight.
Charlton took the lead after 20 minutes when Callum Harriott fired home from 15 yards after the ball had deflected off the back of an Owls defender.
Wednesday had some great chances to again pull level at the death but some frantic defending from Charlton allowed them to book a quarter-final date with the Blades at Bramall Lane on March 8.
2013/14 FA Cup - fifth round
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