Elijah Adebayo impressive run against the Valiants continued with a brace in Staffordshire before David Fitzpatrick's pass to Scott Brown went under the goalkeeper and into the net.
Vale did go level in the first half when Tom Conlon struck a brilliant free-kick past Liam Roberts.
However a very good second-half performance won the game for Darrell Clarke's men as they sit only two points from the EFL League Two play-offs.
Story of the match
On a chilly afternoon in Staffordshire, Walsall dealt Vale an early blow when Adebayo tucked the ball under Brown after a mix-up with defender Nathan Smith.
A ball over the home side's defence caused confusion between Brown and Smith before Adebayo showed his pace to tuck the ball under the goalkeeper and score his first goal since his winner at Oldham Athletic in December.
The Saddlers remained in control as the first-half ticked on, but Vale found themselves level against the run of play just after the half-hour mark through Conlon.
After giving a needless free-kick away, Walsall were pegged back when Conlon's thunderous free-kick beat Liam Roberts from distance, another goalkeeping mistake on the day.
Either side were capable of mustering any more chances, with both back four remaining solid to deny any opportunities.
Conlon's goal did boost Vale's confidence, with David Amoo and Kurtis Guthrie performing well and working well together on many occasions.
However it was the Saddlers who struck next with another goal by Adebayo. Like the first half, the striker was in the right place at the right time to head Tyreik Wright's deep cross into the back of the net.
Adebayo has now hit double figures in his goal tally this season and has scored six career goals against the Valiants. The goal knocked the stuffing out of Vale, with the game being dominated by the away side.
Things got worse for the hosts when David Fitzpatrick's back past was completely misjudged by Brown before trickling under the goalkeeper's foot and into the net.
Mark Cullen did have the ball in the net in injury-time after Scott Burgess had flicked the ball onto the striker, but it was ruled out immediately for offside.
The victory for the Saddlers is their eighth of the season going into the visit of Mansfield Town next week.