Alan Curbishley's side took a deserved lead after 21 minutes when Danish star Claus Jensen ran at the heart of the Everton defence and caused the problems before finding Shaun Bartlett who shot first time.
The South African's effort was blocked by Richard Wright in the Blues goal, but Bulgarian Radostin Kishishev was on hand to clean up and pounce from close-range.
Everton were lacking their cutting edge of recent weeks, but looked to have grabbed a point when they equalised after 70 minutes.
Li Tie played a great ball through to Brian McBride and the American made no mistake from 10 yards.
Charlton, though, came back at The Toffees although it was a mistake from the otherwise outstanding Li Tie.
The Chinese star attempted a pass back but could only find Jonatan Johansson who in-turn fed Kevin Lisbie and the youngster made no mistake in hammering the ball home.
The Addicks were good value for their three points, but The Toffees will be disappointed to have conceded so late in the game.
