It was their eleventh home victory, but they had to be patient with the first goal not coming until the 68th minute via a debatable penalty.
The League's bottom club started brightly, but Luke Rodgers blasted a free-kick over from the edge of the box and Robin Hulbert missed the target from 25 yards.
Tranmere came within inches of the lead on 19 minutes, but an Ian Moore shot from Chris Greenacre's pass was kicked off the line by George Pilkington.
But generally the Merseysiders failed to put much pressure on the visiting goal in the opening half, despite a lot of effort put in by Greenacre.
Paul Edwards, Danny Whitaker and Krystian Pearce were always busy for Vale, but it became more of a backs-to-the-wall task in the second half for the visitors.
Dave Howland was yellow-carded for a foul on Paul McLaren, who went in the book in the opening period for dissent.
Greenacre saw a deflected shot tipped over the bar by Joe Anyon soon after the break. Then McLaren hit the wall with a free-kick.
Rovers sent on Jennison Myrie-Williams in place of Chris Shuker approaching the hour mark to liven things up in attack, before Joe Anyon saved well from Robbie Stockdale and Greenacre.
Edwards conceded the penalty for impeding Myrie-Williams just inside the box, but it looked dubious. Greenacre made no mistake, sending Anyon the wrong way for his ninth league goal of the campaign.
Vale kept going well but could not really trouble home keeper Danny Coyne.
Another home penalty arrived on 84 minutes with Myrie-Williams this time brought down by Jason Talbot, but Greenacre's shot was parried over by Anyon.
However, Moore went clear to double the lead two minutes from time with an angled finish.