Goals at the start and end of the game by Gary Mulligan and Matthew Jarvis were enough for the Gills who are now probably safe from relegation.
Huddersfield were forced into a change before the match as goalkeeper Phil Senior injured himself in the warm up. His replacement Paul Rachubka barely had time to get his bearings before he was picking the ball out of the net.
Matthew Jarvis' left-wing cross hit central defender Nathan Clarke and with the goalie stranded on the floor Gary Mulligan was on hand to grab his first ever goal for the club as he side-footed the ball in from four yards out.
Clarke's day nearly got a lot worse when he appeared to bundle over Mulligan in the box but referee Phil Joslin waved away the appeals.
On 26 minutes Joslin again turned down a penalty claim when Danny Schofield tumbled over Jason Brown and the Huddersfield winger was booked for diving.
Despite going behind so early the away side created the best chances in the first half. Andy Booth twice found himself unmarked in the area but failed to get his headers on target.
His strike partner David Graham did force Brown into a save on the stroke of half-time but his volley from the edge of the area lacked the power to beat the Gillingham goalkeeper.
The second half started at a furious tempo. Mulligan had a good chance for his second when he flicked Jarvis' cross straight at Rachubka.
At the other end Brown made a tremendous one handed save to stop Schofield's close range header.
Gillingham eventually wrapped up the points and probably League One safety on 90 minutes when Jarvis smashed the ball into the top right-hand corner from 25 yards out.