An early through ball from Jose Baxter was hit just too hard for Robbie Weir allowing Walsall keeper Jimmy Walker to gather on the edge of his area, while a low cross from Adam McGurk was just beyond the outstretched leg of Enoch Showunmi at the near post on six minutes.
The first shot of the game came on 18 minutes when Alex Nicholls skipped past a couple of challenges just outside the area before his low shot was well saved by Owain Fon Williams.
Rovers responded with Baxter shooting at Walker from 20 yards after good work from David Buchanan and Weir.
As the half drew on, Tranmere began to take control. A foul on John Welsh drew a free kick 25 yards out on 24 minutes from which it needed a fine diving save from Walker to keep out Baxter's top corner-bound right foot effort, while the combination of Showunmi and Baxter released Weir into the area on 30 minutes but the midfielder lost his balance as he was about to shoot and the Saddlers were able to clear.
A driven free kick from a deep position from McGurk somehow evaded everyone in the Walsall area on 33 minutes and went only a couple of yards wide of the left hand post, and three minutes later Baxter brought another impressive save out of Walker with a shot that went into the ground before looping goalwards following a pass from Lucas Akins.
Welsh and Akins both saw shots charged down on 39 minutes as Rovers pressed from a McGurk throw in and Baxter headed over a deep cross from Dave Raven soon after.
Anton Peterlin fired over for Walsall on 44 minutes, the last effort of a goalless first half.
Fon Williams had to save from Kevan Hurst in the first minute of the second half as the visitors launched a quick counter attack and it needed a well timed challenge from Weir to end the former Chesterfield winger's run towards the area ten minutes in.
There was no one on hand to capitalise on Ash Taylor's flick on that ran past the far post on 57 minutes but a couple of minutes later Rovers took the lead in spectacular fashion. McGurk ran across the area and found Akins on the right. The former Huddersfield player laid the ball off for Weir 25 yards out whose right foot curler found the top right corner beyond the outstretched hand of Walker.
The Walsall keeper had to tip a cross from Akins over his bar on 63 minutes as Rovers pressed for a second and substitute Zoumana Bakayogo, who had replaced McGurk, headed over from an Akins cross on 71 minutes.
Rovers' lead was maintained by a fingertip save from Fon Williams on 72 minutes, the keeper diving to his left to keep out Jamie Paterson's effort. However, he was unable to do anything a minute later, as the from the resulting corner the ball was headed into the net by Saddlers captain Andy Butler.
Bakayogo's cross from Showunmi was just over the striker's head on 76 minutes as Rovers looked to quickly retake the lead and soon after the fresh legs of Mustafa Tiryaki were introduced.
The former Havant and Waterlooville striker, on for Showunmi, made an immediate impact. A pass from Raven went through the area but was kept in by Bakayogo on the left side. He slid the ball across the six yard box to Tiryaki who turned in past Walker for his first goal for the Club.
Labadie replaced Baxter with just a couple of minutes remaining while Walsall's Richard Taundry was inches away from levelling as the game went into five minutes of injury time, striking the bar from a 30 yard free kick.
The Saddlers pressured late on, but Alex Nicholls' low shot across goal was the closest they came as Rovers held on for all three points.