Vale started brightly and threatened to take the lead after only 30 seconds when Paul Harsley's cross found Kyle Perry at the back post, but the midfielder failed to hit the target.
Perry was in the thick of the action again 10 minutes later when his cross was met by Luke Rodgers, who almost converted a cheeky backheel, only for Derek Stillie to make a superb reflex save.
Vale heaped misery on the visitors when Krystian Pearce climbed highest from Harsley's corner to supply Marc Richards with a perfect opportunity to smash home for his first goal for the club.
The Valiants defence was given a wake-up call only a minute after going ahead when Simeon Jackson sprung the offside trap to force a solid stop from Joe Anyon.
Gillingham were gifted the perfect opportunity to level the scores after 31 minutes when minimal contact from Robin Hulbert brought Jackson crashing to the ground inside the area to concede a penalty.
However, after saving a spot kick in midweek, Anyon proved it was no fluke by dashing Jackson's hopes of an equaliser by diving to his right and holding on to the ball.
The Gills continued to try their luck but were let down by poor finishing again when Mark Bentley missed from ten yards after Anyon had spilled another effort from Jackson.
Lee Sinnott's men doubled their lead eight minutes after the break when Danny Whitaker found room just outside of the box to fire an unstoppable shot into the top left corner of Stillie's goal.
Substitute Leroy Griffiths gave the 200 travelling supporters something to believe in 12 minutes from time when he lashed home a close-range volley, but it was too little too late as Vale held on for the win.