Charlton's win came thanks to Danny Green's stoppage-time winner.
Yeovil took the lead on eight minutes when Jon Obika, on loan from Tottenham, scored with an overhead kick after Max Ehmer floated a set-piece into the box.
The Glovers' advantage lasted until the 16th minute when Danny Hollands popped up at the far post to head home a left-wing corner for the visiting Addicks.
Yeovil regained their lead on 49 minutes when defender Paul Huntington nodded in a corner from Ed Upson.
The Addicks then piled on the pressure, equalising on 59 minutes through Yann Kermorgant.
It seemed Yeovil would hold off the late pressure, but in stoppage time the lively Danny Green broke clear on the right and fired his first league goal past the right hand of home stopper Rene Gilmartin and into the far corner.