After knocking out Fulham at Craven Cottage in the third round, the O's had a great chance of more cup glory against a Charlton side that have been dumped out of the competition in three of the last four seasons by teams from lower divisions.
However, when Charlton went in front after seven minutes from Jonathan Fortune's powerful close-range header from Darren Ambrose's free-kick, it looked like a routine win for the Premiership team.
But Orient, beaten only once away this season, gave Charlton a real fright and had three glorious chances to level the scores before the interval. Gary Alexander headed just wide, then shot over the bar and Joe Keith also went close.
Orient got a deserved equaliser after 53 minutes when Lee Steele's shot crept into Thomas Myhre's net.
Charlton boss Alan Curbishley threw on three substitutes at the same time and it made a big difference in galvanising his team, and Orient goalkeeper Glyn Garner had to make two great saves to deny Jerome Thomas and Jay Bothroyd.
Orient ran out of steam a little and had to scramble an Ambrose shot off the line but they were still dangerous with Matt Lockwood firing across the Charlton goal and Daryl McMahon putting in a weak header from a good position.
Just when it looked as though the O's had done enough to gain a deserved replay, Charlton struck the winner when Matt Holland rolled a free-kick to Bothroyd whose 20-yard shot took a deflection and went through the hands of the unlucky Orient goalkeeper to win Charlton a place in the fifth round.