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Bradley Dack scored on his return to action for the Gills.
Dack, back after five weeks out with a hamstring injury, was involved in the Gillingham development team as they beat AFC Wimbledon 3-2.
Young defender Finn O’Mara headed home the winner in stoppage-time to complete a comeback win.
Returning midfielder Dack scored just before the break as his free-kick took a deflection to deceive Dons keeper Will Mannion.
It was a dominant first half performance from the Gills, led at the back by John Egan, who was also getting in valuable minutes after injury.
Egan won everything in the air, keeping a young defence in check, including the impressive O'Mara who played alongside him at central-half.
Teenager Darren Oldaker wore the captain’s armband in a team that also included Jermaine McGlashan, Emmanuel Osadebe and Cody McDonald – another player making a return from injury.
McGlashan was playing upfront and put in good crosses for Jake Hessenthaler and McDonald, but neither could find the target. He had a shot of his own blocked during a lively opening.
Egan did have a header on target, from a Hessenthaler corner, but that was well saved by Mannion.
VIDEO: Jermaine McGlashan scored for the Gills in the 3-2 win.
Dack was withdrawn at the break, after an energetic display, and both Egan and McDonald came off around the hour mark. But by then Wimbledon had turned the game around.
Jason Stripp levelled the scores for Wimbledon before Callum Wilson fired into the top corner from 25 yards with a shot that gave keeper Glenn Morris no chance.
Morris made a couple of good saves but Gillingham took charge of the game in the latter stages.
In the final minute McGlashan, to the delight of those watching including Gills chairman Paul Scally, bundled home the equaliser from a corner.
Moments later, with almost the last action of the game, O’Mara powered home a header to win it for the Gills.
Gillingham XI: G Morris, Thompson, Emptage (Lawford 70mins), Egan (Welch 60mins), O'Mara, Hessenthaler, Oldaker, Osadebe, Dack (Cundle 46mins), McDonald (Stevenson 60mins), McGlashan.