Vale were made aware of danger man Matthew Jarvis' presence in the opening minutes as he went close twice to wake up the sleepy home defence.
After being dominated for the early part of the match, Vale put together a slick move on the edge of the box resulting in a Ross Gardner shot that was helped on by Danny Whitaker to give his side a ninth minute lead.
The Valiants should have doubled their advantage after a quarter of an hour when Jeff Smith's left-sided cross found Leon Constantine waiting in the middle only for the striker to fluff his ten-yard shot.
Gillingham would have been hoping to turn the tide after the break but it looked like it would be more of the same as Constantine broke, setting up Paul Harsley for what should have been a goal if not for a desperate last ditch tackle by Brent Sancho.
Former Port Vale loanee Gary Mulligan almost turned provider for Guylain Ndumbu-Nsungu when he threaded his team-mate into a shooting position but the chance was fired wide in the 63rd minute.
With the introduction of Stefan Moore adding little to Martin Foyle's front line, Smith took it upon himself to contribute from midfield with his fizzing 25-yard low drive narrowly going wide.
Smith was at the forefront of the Vale attack once more in the 71st minute when he cut inside his marker on the edge of the box to float a shot goalwards only for Kelvin Jack to fly to the rescue.
Despite pulling off the save, Jack turned villain seconds later when another wayward goalkick fell to the feet of Whitaker who calmly played through Constantine for his 14th of the season.
The Gillingham goalkeeper's Jekyll & Hyde character showed itself again when, after Constantine laid on a perfect cross for the arriving Moore, Jack sprung into action by saving from point blank range.
However, it made little difference to the final result.