The winger struck from close range in the 79th minute following a positive run and cross from the right flank by substitute Jaime Peters which left him with the easy task of tapping home.
The game had been heading for a stalemate with chances few and far between as defences were on top.
Jay Harris had Chester's first effort of the game in the 11th minute when he hit a shot from distance that flew just past the post.
The home side had a decent claim for a penalty turned down on 20 minutes when Ritchie Partridge appeared to be tripped by Stuart Lewis, although the City winger did appear to go down rather easily.
The Gills were forced into a change at half-time with Simon King, who had earlier fallen awkwardly following an aerial challenge with Chester keeper John Danby, being replaced by Garry Richards.
The substitution did not seem to knock the visitors out of their stride as they exerted pressure on Chester early in the second half.
Simeon Jackson shot harmlessly over the bar with a good chance inside the penalty area, and Nicky Southall curled a low effort on 55 minutes that Danby saved low down to his right.
Chester were probably glad to see the back of the not yet fully-fit striker Dennis Oli, who had proved difficult to handle until he was replaced on 63 minutes by Gary Mulligan.
Ryan Lowe hit a shot from distance which was easily saved by keeper Simon Royce who was also on hand to palm away an effort from Partridge which was creeping inside the near post, as Chester got stronger as the second half progressed.
But it was the Gills that struck through Barcham's late goal, although the home side were unfortunate when, four minutes from time, Kevin Roberts' header was cleared off the line by Stuart Lewis, the ball striking the post on its way out.