The only goal of the game arrived in the 33rd minute when Vale defender John McCombe inadvertently headed into his own net to put the home side in front.
Vale, under the stewardship of caretaker duo Dean Glover and Andy Porter following Lee Sinnott's departure on Monday, had made five changes to side that suffered a 4-1 hammering at Macclesfield the previous week.
And it was they who looked the brighter side early on with Marc Richards heading a decent chance over from Shane Tudor's corner in only the fifth minute.
The hosts, meanwhile, struggled to gain a foothold in the game as the first half progressed, although they did force a number of set-pieces that had Vale defending in numbers.
It was no surprise therefore that a free-kick should provide the source of Gillingham's opener, although it arrived with huge chunk of fortune.
Mark Bentley met Charlie Daniels' free-kick with a near-post flick and the ball bounced off unfortunate defender McCombe and over the line despite the best efforts of keeper Joe Anyon.
The visitors almost conceded again shortly after the interval when on-loan debutant Andrew Bircham beat full-back Sam Stockley for pace only to see his cross narrowly evade a diving Bentley.
But this was hardly proving a vintage performance by the home side despite an impressive debut by Bircham and with 15 minutes remaining goalkeeper Simon Royce did well to hold Richards' fierce 20-yard free-kick.
As Vale continued to chase the equaliser, gaps began to appear in their defence and in the 81st minute Simeon Jackson squeezed in a shot that forced Anyon to push the ball onto his near post.
That proved to be the final chance of note as Vale began life after Sinnott with a defeat.