Vale nearly snatched an unlikely draw after two late goals but hosts Gillingham held on to secure all three points.
Micky Adams made two changes with Dan Jones replacing Rob Taylor and Louis Dodds coming in for Jennison Myrie-Williams. Newcomer Billy Knott was named as a sub. In a well-matched opening period, both sides looked to impress but without really troubling either keeper in muddy and rainy conditions.
However, that changed with two minutes to go before the break as Ade Akinfenwa headed in unchallenged to give the Gills the lead. It was his fifth career goal against the Valiants.
Vale rallied in the second-half and Pope had a claim for penalty. Then Dodds had a clear chance ony to fail to trouble the keeper. But Vale were then grateful to goalkeeper Chris Neal who pulled off a terrific double save to prevent Gillingham stretching their lead.
However, that work was undone as Vale once again left Akinfenwa unmarked and he duly headed in to make 2-0 to the home side on the hour mark. Vale responded with a double substitution but three minutes later, Gillingham seemingly wrapped up the three points as Cody McDonald’s good finish put the home side 3-0 up.
The Valiants then introduced Billy Knott for his debut as he replaced Anthony Griffith and the game looked well and truly over by that stage.
But inspired by sub Knott, Vale rallied. Chris Robertson headed in his sixth of the season to make it 3-1 with eight minutes left and sub Jordan Hugill netted his fourth Vale goal of his career with three minutes left.
Those goals inspired Vale to pour forward with Tomlin and Loft going close but despite the late pressure and five minutes of injury time, the Vale were unable to score the all-important third that would have earned them a share of the points.
Vale: Neal, Grimmer, Davis, Robertson, Jones, Dodds (Hugill), Griffith (Knott), Lines, Loft, Tomlin, Pope (Williamson)
Subs: Johnson, Birchall, Yates, Myrie-Williams
Attendance: 6,356 (202 away)