The Gills only needed a point to seal the League Two championship and duly went ahead after just 12 minutes as Deon Burton neatly volleyed past John Sullivan after the Dons defence had failed to clear Chris Whelpdale's cross.
Whelpdale was again the provider when former Dons striker Danny Kedwell headed in to double their advantage midway through the first half for his 16th goal of the season.
Following a lacklustre opening 45 minutes the Dons looked more like the team who did the double over the Kent side last season.
Luke Moore, Chris Hussey and Pim Balkestein had all squandered good opportunities to pull one back for the visitors before Jack Midson halved the deficit with 25 minutes remaining, finishing from close range after neat build-up play between Jonathan Meades and substitute Charlie Strutton.
Meades then slotted home from Midson's cut back to level the scores after 82 minutes, before sub Gary Alexander almost won it but his volley cannoned back off a post - with the Dons subsequently slipping into the bottom two heading into the final weekend of the season.