Terrible defending gave Vale the edge in the first half, but they were under pressure in the second, especially after defender Krystian Pearce was sent off for a second yellow card on the hour.
Vale shook Hartlepool with two goals in the opening 15 minutes, then when they had to defend as the home team tried to fight back, keeper Joe Anyon was in great form.
Chris Herd was the hero at the other end first as he struck both Vale's early goals.
First, on three minutes, he was at the end of a speedy break from the back to place his low shot from the edge of the area into the bottom left-hand corner.
And on 15 minutes he hit exactly the same spot, this time with an angled shot from wide on the right after being fed by Tobias Mikaelsson.
Hartlepool were in a right old mess at the back as Vale threatened to score every time they broke, but when the home team at last managed to create some chances, Anyon was in top form.
He produced good saves to keep out shots from Alan Thompson and Richard Barker and a brave block at the feet of Anthony Sweeney after his overlapping run on the left was spotted by Joel Porter.
But Anyon's best save came minutes before half-time when he threw himself to his left to tip a curling free-kick from Thompson around the post when a goal again looked certain.
Pearce's red card came after a handball following a yellow for a foul in the first half and on 68 minutes Hartlepool narrowed the gap with a header from Barker after Thompson's chip.
Three minutes from time, Sweeney forced the ball in after Vale failed to clear a corner and in the last minute, Barker headed his 16th goal of the season from Thompson's corner for a win that looked unlikely for an hour.