The Republic of Ireland international, who has joined on loan from Leeds for a month, found the corner of the net with virtually the last kick to give Blues the points in front of a 2000 travelling support.
The goal ended Charlton's unbeaten home record and pushed Blues into the automatic promotion places before the rest of the Championship games kicked off.
Town were forced into a change just 20 minutes before kick-off, Luke Hyam picking up an Achilles injury in the warm-up, Stephen Hunt stepping up from the bench as the replacement.
New signings Noel Hunt and Sean St Ledger were among the substitutes, with the game starting at a blistering pace, Luke Chambers and Daryl Murphy both going close for Blues inside the first four minutes, while Charlton also had an opening with Johann Gudmundsson firing over.
Gudmundsson threatened again from Igor Vetokele’s chest down but Tyrone Mings cleared the danger.
Callum Harriott sent an ambitious 25 yarder wide for the home side but had a much better effort moments later, Bart Bialkowski beating his effort away at his near post.
Harriott forced Bialkowski into a comfortable save with another left foot effort, the striker continuing to carry a threat to Blues’ goal, this time turning away from Mings and sending a right foot strike just wide.
Bialkowski held firm from Morgan Fox’s effort, then former Town Academy ‘keeper Nick Pope beat away Paul Anderson’s strike from distance as Blues threatened on the half hour.
Hunt swung in a dangerous free-kick that evaded Murphy at the far post, Bialkowski again alert in goal for Town to deny Francis Coquelin from close range after the midfielder had burst onto a pass in the box.
A clever free-kick created space for David McGoldrick, his shot going a yard wide, Chris Solly then testing Bialkowski with a vicious left footer from the edge of the box.
McGoldrick had the last clear chance of the first-half, his header pushed behind for a corner by Pope to leave the scorers untroubled at the break.
It was McGoldrick who got the second-half underway with a curler from the edge of the box that failed to trouble Pope. The ‘keeper had an anxious look back seconds later though when Mings weaved his way past three Charlton players before firing just wide.
Mings came to Town’s rescue soon after, robbing Vetokele as the frontman looked to break the deadlock.
Chambers defended well from Solly’s cross to partially clear the danger, Hunt showing a great touch to take the ball on his chest and head back to Bialkowski to finish the job for Blues as the hour mark passed.
Murphy was close with a right foot curler, Gudmundsson denied at the other end as Town smothered his shot after Charlton broke then Pope was in the right place to hold McGoldrick’s snap shot.
The chances continued to come at either end, Harriott miskicking when in a great position from Vetokele’s pull-back, Gudmundsson firing over from 18 yards.
Conor Sammon replaced Hunt for the last 15 minutes, Jonathan Parr getting back to quell the danger from Vetokele as the points remained there for the taking.
Noel Hunt was handed his debut eight minutes from time, Anderson making way. McGoldrick tested Pope again before Sammon could have won it for Blues but Andre Bikey rescued his side with a terrific last ditch challenge, the Town frontman then inches away from Parr’s cross as Town finished the more likely winners.
It looked as though Town would have to settle for the draw though until Hunt sent Blues into dreamland with that last minute winner.