Alan Curbishley made no excuses for this defeat, admitting that Gillingham thoroughly deserved the victory in front of a near full house at Priestfield.
The Gills beat Sheffield Wednesday and Bradford City - then in the Premiership - four seasons ago but this eclipsed both of those triumphs as they did it the hard way after handing Charlton the lead after only 34 seconds.
Gillingham were punished for a hesitant start and it was Nyron Nosworthy's uncharacteristic mistake that allowed Paul Konchesky too much time and space, and his cross to the near post bounced off Ian Cox and into the net.
To their credit Gillingham responded in positive fashion. Despite being without eight first choice players they carried the fight to Charlton and the game was won and lost in a tremendous 17-minute spell.
Local boy Danny Spiller performed heroics in the Gills midfield minus the injured player-manager Andy Hessenthaler and Mark Saunders, and it was he who set up the equaliser for verteran Tommy Johnson. He shrugged off Chris Perry to fire inside a Dean Kiely's left hand post.
Two minutes later Gillingham were in front. Again Johnson was involved setting up Nicky Southall and his pinpoint cross picked out big striker Mamady Sidibe to power a header over Kiely.
Gillingham were forced to include a rookie French goalkeeper Bertrand Bossu for his full home debut.
He kept out a header from Carlton Cole before Gillingham made it 3-1 as skipper Paul Smith scored his first of the season with a 25 yard right footed effort, as Kiely looked slow to move.
Paul Shaw then fired into the side netting just before half time.
Charlton, without influential midfielder Scott Parker because of injury, left Paolo Di Canio on the bench until just before the hour but Kiely had to produce three fine saves to stop Charlton being further embarrassed.
He blocked an effort by Nosworthy, kept out another with his legs from Sidibe and then denied Johnson a second, making partial amends for his earlier mistakes.
Johnson left the field to a standing ovation and was replaced by new signing Darius Henderson, signed the day before from Reading.
Bossu hardly had a shot to save in the second half until Curbishley's men suddenly picked up the pace. He kept out two close-range Jonatan Johansson and then made an even better save to stop di Canio making it 3-2.
The enigmatic Italian struck a post with four minutes left before Cole made the scoreline respectable firing home as the clock ticked into stoppage time, after Bossu had again done well.
Boss Andy Hessenthaler said: "It's one of my best results since taking the job. I thought we played some great football and were awesome. Every one of my players did great.
"Bertrand burst into tears in the dressing room as it was a very emotional day for him, and now we hope that we can get another decent draw on Monday."