A strong travelling support of 322 Gills saw the Gills crash to an all-too-familiar away defeat, as two goals in quick succession put paid to their hopes of another good away result.
Lee Frecklington's 12th minute header was quickly added to by Danny N'Guessan's solo effort just two minutes later as Gillingham showed their defensive frailties on the road once again.
The Gills managed to steady the ship thereafter, but with top scorer Simeon Jackson still ruled out through injury, the strike partnership of Mark McCammon and Gary Mulligan failed to trouble Rob Burch in the Imps' goal.
The defeat sees Gillingham drop three places to 11th in League Two, two points adrift of the playoff zone, and four points off the automatic promotion places.