It was Obika's second late winner in as many home games after he scored against Leeds at The Valley, with this victory taking Charlton's unbeaten run to six matches.
Kevin Doyle had headed in an equaliser after Dorian Dervite had opened the scoring for the Addicks, but Obika had the final say.
Addicks boss Chris Powell said: "Obika shows the value of having a squad. He has been top class since he came into the dressing room.
"He is good finisher, when he doesn't start he wants to be involved, he always gets chances, which is a good trait for a striker.
"On top of that Jonathan is a good character and deserves hero status for the day."
Powell also believes his side deserved all three points from the game.
"On the balance of chances we deserved the win," said the Addicks boss.
"They had two, the Karl Henry shot and the goal but apart from a few crosses our keeper has not had a lot to do. We had the better of the chances and these lads never give up and they dug in again."
- Sports & Recreation
- Chris Powell