Both sides were among the favourites for promotion at the start of the season, but they are still well off the pace after sharing the spoils at Priestfield.
Gillingham thought they had made a dream start in the fifth minute when Danny Spiller put the ball in the net after it had fallen to him from a deflected Neil Harris shot, but their joy was short-lived as the linesman ruled the effort out for offside.
City had the ball in the net five minutes later and it counted. Scott Murray controlled the ball on his chest, took it round Ian Cox in the box before tapping his shot past Jason Brown and into the net.
City were forced into changing their keeper on the half-hour mark when Adriano Basso was injured as he parried a 25-yard Danny Jackman free-kick round the post. He injured his hand in making the save and played no further part in the encounter.
Steve Phillips, his replacement, was poised for his first action of the afternoon on 38 minutes as a long kick from Brown caught City's defence napping but Bradley Orr recovered well to challenge Harris in the box just as he was about to shoot.
The Gills' half-hearted claims for a penalty were waved away by referee Andy D'Urso.
Gillingham seemed devoid of ideas in the second half and they only managed an equaliser thanks to a gift in the 69th minute when Phillips somehow failed to keep out Mike Flynn's 35-yard free-kick.
Neither side looked capable of winning the match in the closing stages and avoiding relegation rather than moving up to the play-off places seems a more realistic task for both sides this season.