Old warhorse Rod Wallace hit the opener before midfielder Paul Smith killed off battling Wednesday who hit the woodwork three times and failed to put away the chances.
Wednesday fell behind in the fourth minute after woeful defending. Marlon King was given space to fire in a low shot, Kevin Pressman managed to get a hand to the ball but could only deflect it into the path of Wallace who finished from close range.
Gillingham escaped in the 18th minute, the hardworking Matt Hamshaw cutting in from the right to fire in a stinging drive from the edge of the area, the ball looping off Leon Johnson before crashing against the underside of the bar.
Big defender Tony Crane had a close-range header snatched by Jason Brown and Wednesday skipper Trond Soltvedt saw his low drive smothered by the Gillingham keeper as fired up Wednesday battled for an equaliser.
Full-back Ryan Green was foiled by Brown as he palmed away his long-range strike before Wednesday hit the woodwork again, nine minutes before the interval, Shefki Kuqi steering in a low cross to Gerald Sibon who cracked a left-foot volley against the bar.
Incredibly, Wednesday were denied by the woodwork again on 41 minutes, Kuqi beating Brown with a low shot from the edge of the box, the ball crashing against the foot of the post.
Kuqi squandered a simple chance to level matters in the 53rd minute heading an Allan Johnston cross wide from six yards before Smith killed off Wednesday in 74th minute.