After a goalless first half, this fixture burst into life with a double strike from Gills' hitman Darius Henderson, one either side of Nathan Ellington's 21st goal of the season for Wigan.
The turning point of the match however was the introduction of striker Mamady Sidibe at the re-start. The Mali striker was a constant thorn in the Latics' defence, his pace and power proving too much for the visitors.
The opening was dominated by several half chances. Ellington and strike-partner Jason Roberts combined well on the edge of the box, with Roberts shooting over the bar on seven minutes.
The deadly duo were at it again on 20 minutes but once again Roberts was off target.
The Gills were not overawed however with Nyron Nosworthy doing well on the right but his effort was straight at John Filan.
Midway through the half, Matthew Jarvis' trickery almost caught out a static Latics' defence, but his shot was too close to Filan.
On the half-hour mark Henderson challenged Filan for a high ball but managed to catch the keeper. Both were yellow carded after the ensuing melee involving several players from each side.
Two minutes after the break, Nosworthy crossed for a cushioned header from Henderson which Andrew Crofts hit just wide.
With the Gills in the ascendancy, Crofts had another effort go wide but his side took the lead with their next attack.
Sidibe's menacing persistence on the left enabled him to muscle his way past Nicky Eaden and his cross fell to Henderson who netted from close in.
Gillingham's lead was to last all of two minutes. From out of the blue, Ellington lashed in from 25 yards to pull Wigan level.
The woodwork was then to deny the Latics, firstly, with Steve Banks in the Gills' goal stranded, Gary Teale's curling effort only found the bar.
Then on 70 minutes with an open goal at his mercy, Roberts could only head on to the bar from Lee McCulloch's knock back.
With both sides going for the victory, Sidibe's persistence once again allowed the ball to reach Henderson, who lashed in past Filan from an acute angle for the winner.