Ellington struck after 17 minutes when strike partner Jason Roberts latched on to a ball from midfielder Jimmy Bullard and crossed for the powerful striker to claim his 14th goal of the season with a clinical finish from six yards.
Wigan made it a tough baptism for Stan Ternent who was taking charge of the Gills for the first time and their flowing football frequently had the visitors chasing shadows all over the pitch.
Shots rained in towards the Gillingham goal but Wigan couldn't find the finishing touch that brought them five goals in their last home outing against Preston.
The pattern continued after the break with Gillingham defending well and relying on the break to catch Wigan on the back foot.
They almost fell further behind after 63 minutes but Paul Gallacher produced a fine save to deny McCulloch.
But McCulloch was to have the last laugh two minutes from time when he converted substitute Michael Flynn's cross at the far post to give the scoreline a far more realistic appearance.