John Sheridan's side went into the clash knowing a solitary point would be enough to secure the title but they claimed all three at the b2net Stadium to deservedly seal top spot, with second-placed Bury drawing 3-3 at Stevenage.
For the Gills, it was a case of so near, so far as they finished in eight spot, narrowly outside the play-off places by virtue of goal difference.
The home side got the breakthrough they craved in the 54th minute when hesitation in the Gillingham defence allowed Danny Whitaker to take the ball round Alan Julian and score from a tight angle.
Tommy Lee made another good save to keep out a Danny Jackman drive in the 65th minute, but shortly afterwards Adebayo Akinfenwa put Cody McDonald in on the right and he forced the ball in off the keeper for his 25th goal of the season.
Gillingham looked the more dangerous team but 13 minutes from time Jack Lester turned in a Scott Griffiths cross from the left, and the full-back then set up Deane Smalley five minutes later for the goal that cranked up the celebrations.