On a dramatic night the Shrimps were grateful to a first half penalty save from Christoffer Mafoumbi before goals from Steven Old and an injury time strike from Carlos Mendes-Gomes gave them the win.
The game swung from end to end in the first half with Walsall having the best chance to take the lead when they were awarded a penalty on 22 minutes.
Wes McDonald was brought down on the edge of the area by a clumsy challenge from Carlos Mendes-Gomes.
The same player stepped up to take the spot kick but saw his effort superbly saved by Christoffer Mafoumbi.
From there it was Morecambe who had the better chance as they produced some great chances on the counter attack.
Ryan Cooney drilled a shot straight at Liam Roberts after a smart turn in the box and Adam Phillips drilled a fierce left foot shot inches wide from the edge of the box.
Phillips went close again when he was found in the box but saw his final shot come off the top off the Walsall crossbar.
The second half burst into life after Old headed the Shrimps into the lead on 68 minutes.
Jordan Cranston swung over a deep corner and Old was left unmarked to direct the ball past Liam Roberts for his fourth goal of the season.
Walsall hit back with Caolan Lavery missing the target from a great opportunity and then heading just over the bar from close range.
The Saddlers enjoyed the greater share of the pressure with the Shrimps defending well until the 94th minutes when Dan Scarr got ahead of his man to divert a cross onto the post with the ball rebounding straight into Mafoumbi’s hands.
And Derek Adams’s side took full advantage of the good fortune as they sealed the points moments later.
Morecambe broke clear and Mendes-Gomes made the most of the space he was given to turn inside his man and curl a left footed effort past Roberts tout the seal on a good night for the Shrimps.