Shaun Williams' penalty had given the Dons a half-time lead but Kermorgant nodded in his first goal for the club in the 75th minute to cement the Addicks' place at the top of League One.
The Dons dominated the first half and Luke Chadwick drilled a snap-shot narrowly wide before Stephen Gleeson's 25-yard curler was well-saved by Charlton goalkeeper Ben Hamer.
Williams deservedly put the Dons ahead from the penalty spot after 21 minutes, confidently stroking home his first goal for the club after Chris Solly had scythed down Dean Lewington in the box.
Hamer then produced good saves to keep out Darren Potter's fierce low drive and Williams' volley on the stroke of half-time. Charlton improved after the break and Paul Hayes' rasping volley was well-saved by David Martin before Dons defender Mark Beevers miscued a free header from seven yards.
Kermorgant equalised for the Addicks to set up a pulsating finale when his near-post header from fellow sub Danny Green's cross hit the inside of the post and rolled across the line.