Charlton were three minutes from a sobering defeat at Stevenage until Chuks Aneke rescued the tie with a late equaliser and Scott Fraser won it in a penalty shootout.
Fraser settled the comeback after Jake Taylor had seen his penalty saved, and the Addicks have made it into the last 16 of the competition for the first time since they were in the Premier League with Alan Curbishley was in charge.
Ben Garner’s League One side had gone behind to a Luke Norris penalty midway through the first half when Richard Chin misjudged the flight of a swirling cross and handled the ball.
Striker Norris sent goalkeeper Joe Wollacott the wrong way from the spot and Steve Evans’ League Two promotion chasers thoroughly deserved the lead.
Norris had already fired one fine opportunity over and they missed more chances to stretch clear before half time. The best of them fell to Taylor but his hurried finished was saved by Wollacott.
Taylor then hit the woodwork when what appeared to be a cross clipped towards the back post drifted onto the bar. Stevenage carried the greater goal threat into the second half. Wollacott saved from Danny Rose and Taylor fizzed another shot wide.
They ought to have had the tie sewn up but the visitors improved after Garner made a quadruple substitution with just over an hour gone.
Ryan Inniss headed against the bar as they produced a strong finish and Aneke found the goal to take the tie to penalties.