The Saddlers dominated the first half and arguably displayed some of their finest passing and attacking football of the campaign, but failed to get that all-important goal.
Then, on the stroke of half-time, a Dan Scarr mistake allowed Cole Stockton to race through and put the visitors ahead.
With the game finely poised in the second half, Walsall again had their moments but struggled to find the final pass. Morecambe grew into the game and finally added a second after 77 minutes through Yann Songo’o.
The hosts could not find a way back into the game in the closing minutes and ended their home campaign with a loss.
Brian Dutton named an unchanged starting XI and squad, sticking with a 4-3-3 formation.
Assistant manager Mat Sadler again was not involved in the 18 as he focused on his coaching responsibilities, while Derick Osei Yaw, Rory Holden, Stuart Sinclair and Callum Cockerill-Mollett were all absent.
This meant youngsters Joe Willis and Jack Nolan kept their places on the bench.
Derek Adams made four changes to his team, starting in a 4-1-4-1 formation.
Former Wolves striker Liam McAlinden was one of the players that came into the side as the visitors only named five substitutes.
The Saddlers made a fast start and pressed Morecambe high up the pitch. A Hayden White cross from the right almost caught goalkeeper Kyle Letheren napping but he managed to tip it over the bar.
But some sustained pressure from the Shrimps saw the Saddlers camped in their own half as they defended a handful of corners and set pieces.
In what was a fairly entertaining start to the game, Tyreik Wright then turned on the style. A nice passing move between Liam Kinsella and White saw the former feed Wright on the edge of the box. He danced between three defenders and raced towards goal but had his effort smothered as Morecambe recovered.
The young winger seemed to inspire his team-mates who began to get on the ball. Sam Perry, Kinsella and Emmanuel Osadebe all saw plenty of it and passed the ball around nicely. Osadebe then delivered a wonderful free-kick that both Scarr and Max Melbourne were inches away from connecting with at the far post.
Wes McDonald then went on a tricky run down the left and delivered a superb low cross across the face of goal. Kinsella was arriving at the far post but was just short of reaching the ball.
As the game edged towards the final five minutes of the first half, the barrage of Walsall attacks was relentless. This time White went on a marauding run down the right and after seemingly losing the ball in the box a Morecambe clearance ricocheted off him and landed at Josh Gordon’s feet. His shot at the near post whistled just wide.
For all their pressure, However, it was a simple mistake that meant Morecambe found the first goal. Scarr miscontrolled the ball on the edge of his box and allowed Stockton to steal it and curl a neat effort beyond Jack Rose.
The strike came on the stroke of half-time and as a result the visitors entered the break with the lead.
As the second half got underway it was much of the same from Walsall who were pushing for their first goal of the afternoon. Some nice play between McDonald and Wright saw the latter deliver a low cross that was begging for a touch.
Perry then crossed first time from the loose ball and found Gordon five yards out, but he was stretching for the ball and directed his header over the bar.
As the game passed the 60-minute mark a handful of Saddlers set pieces came and went as they struggled to find that final ball when attacking. Morecambe, however, saw very little of the ball and created nothing going forward as they hung on to their lead.
A rare foray forward for the visitors, however, almost resulted in a goal when substitute Ben Pringle crossed with his first touch of the ball and found Toumani Diagouraga who, from 10 yards, smashed his effort wide.
Caolan Lavery was introduced after 65 minutes as Walsall looked for the equaliser. They also changed to a 4-2-3-1 formation as McDonald moved behind the striker and Osadebe moved to the left wing.
By this point, however, the Shrimps were starting to have more joy and saw a handful of half-chances come and go. Overall, they were seeing more of the ball and causing Walsall some issues.
Then, after 77 minutes, they found a second. First, Sam Lavelle met a corner but his header was saved well by Rose, before Songo’o reacted quickest to head home the loose ball from two yards.
That goal essentially killed the game off and although Walsall saw plenty of the ball, they failed to create anything meaningful with it.
After five minutes of added time they could not find a way through and fell to a 2-0 defeat.
Walsall: Rose, White, Clarke, Scarr, Melbourne, Osadebe, Kinsella (Bates, 82), Perry, Wright, Gordon (Lavery, 65), McDonald.
Subs not used: Roberts, Norman, Leak, Willis, Nolan.
Morecambe: Letheren, Cooney, Lavelle, Knight-Percival (Davis, 92), Hendrie, Songo’o (Kenyon, 92), Lyons, Price (Pringle, 62), Diagouraga, McAlinden (Denny, 89), Stockton.
Subs not used: Halstead.