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Managerless Gillingham ended their poor home campaign with another defeat.
Goals from Joe Aribo and Josh Cullen put the play-off bound Addicks in charge at the break.
The Gills - who sacked manager Steve Lovell on Friday - were unable to respond after the interval but at least the day ended with any lingering fears of relegation over, courtesy of results elsewhere.
Gillingham, who were unchanged from their Easter Monday match at Bradford, were lively at times but without an end product.
Leo Da Silva Lopes and Regan Charles-Cook both got into good positions for the Gills but couldn’t beat visiting keeper Dillion Phillips.
The game’s opening goal came on 24, for Charlton, shortly after Tahvon Campbell’s rising effort had been turned over the bar by Phillips.
Ben Purrington’s low ball into the box hit the leg of Max Ehmer and fell invitingly for Aribo who then struck a low shot through the legs of Connor Ogilvie and past an unsighted Tomas Holy.
Charlton defender Naby Sarr twice went close for the visitors, keeping Holy alert with a free-kick before diverting the ball off the crossbar.
A second goal was scored by Cullen – his first for the club – as he picked his spot after Holy had spilled an initial effort from Jonny Williams.
Igor Vetekole went close to a third for Charlton early in the second half, denied by Holy with his first effort and seeing his follow-up deflected wide.
Purrington was even closer with his 57th minute effort, racing into Williams’ low cross at the far post, but Holy stood his ground and made a good save to keep the Gills in the game.
Substitute Dean Parrett twice shot wide for the hosts but clear-but chances remained few and far between.
Former Gills striker Josh Parker played the final 12 minutes for the visitors, taking to the field to a mixed reception from fans.
Eaves tried an overhead kick with 10 minutes left but it wasn’t anywhere close to troubling the scoreline.
Cullen had a great opportunity to grab a third in the 88th minute, as Charlton broke, but he headed Aribo’s cross over.
Mark Byrne fired wide for the Gills with a minute to go.
Gillingham: Holy, O’Neill, Fuller, Ogilvie, Ehmer, Byrne, Lopes, Charles-Cook (Parrett 64mins), List (Rees 71mins), Campbell (Eaves 46mins), Hanlan. Subs: Hadler, Garmston, Lacey, Oldaker.
Charlton: Phillips, Dijksteel, Pearce, Vetokele, Pratley, Purrington, Aribo, Williams (Parker 78mins), Sarr, Cullen, Lapslie (Morgan 86mins). Subs: Maynard-Brewer, Page, Doughty, Forster-Caskey, Reeves.
Attendance: 8,047 (2,306 away)