Macclesfield made a bright opening and went close in the third minute when playmaker Terry Dunfield sent a sharp shot inches wide from the edge of the box.
However, their defence was caught napping in the 18th minute when Adam Miller was left unmarked to send in a firm downward header from the six-yard line. Defender Izak Reid was on the goal-line but could only head the bouncing ball into the roof of his own net.
Macclesfield came to life in first-half injury-time when striker Francis Green turned sharply in the box only to drive a low shot off the foot of the far post.
Moments later Dunfield again went close with a 20-yard shot that skimmed over the crossbar.
After the break Green set up central defender Matthew Flynn who put a woeful attempt well over the bar from 12 yards.
Sub Simon Yeo might have scored with his first touch, but instead sliced horribly wide from close range.
The Gills should have extended their lead on 67 minutes when Macc keeper Jon Brain dropped to the ball at the foot of Miller, who poked a sharp chance against an upright.
Yeo then broke through for Macc, but could only fire wide from 15 yards.
In the dying stages Gillingham looked dangerous on the break, Nicky Southall sliding a shot inches wide of the far post and Miller forcing a stunning save from Brain with a perfectly-timed snapshot from 15 yards.