Despite Frank Nouble netting a stoppage time penalty the Gills were beaten on their travels for the second time in four days, this time on a damp, dreary afternoon at the Globe Arena.
Not for the first time this season the Gills put in a reasonable performance but failed to pick up a point, both of which were decent strikes once again but defensively preventable.
Unfortunately at the other end they struggled to test home keeper Barry Roche throughout the 90 minutes.
Despite having plenty of the ball they just couldn't turn possession into clear cut chances and it allowed Morecambe to record their third home victory of the season.
Gillingham manager Andy Hessenthaler chose to name an unchanged starting XI from Tuesday night's trip to Swindon.
There was one change on the bench where Joe Martin
, returning from susension, replaced Dean Rance. The first chance of the game fell to the home side in the fifth minute, Laurence Wilson launched the ball forward, Jason Price knocked the ball down for Gary McDonald who slammed his shot wide from the edge of the area.
In the eighth minute Morecambe took the lead when a cross from the right&nbsp;was half-cleared by Curtis Weston to&nbsp;Garry Hunter around 20-yards out and his speculative lob/volley dipped over Ross Flitney and bounced in off the underside of the bar.
The Gills tried to respond and began to create half chances, the first of these was Chris Whelpdale
drilling a low shot off target.
In the 16th minute Jo Kuffour played the ball out wide to Whelpdale who knocked a great ball across the face of goal which was inches away from the lunging Charlie Lee
As the Gills began to control matters Luke Rooney struck two shots wide of the mark in quick succession, then on the half-hour he finally forced Barry Roche into a low save after his corner found it's way back to him.
The next to have a try was Lee who fired wide from around 25-yards.
H/T: 1-0 Morecambe suffered the curse of the captain's armband during the game, in&nbsp;the first-half Will Haining had to be replaced by Kieran Charnock, then early in the second-half Wilson was injured with Izak Reid taking over from him.
After a slow start to the second-half the Shrimps broke forward in the 55th minute, Price and Lewis Alessandra swapping passes before the former saw his curling cross cut out by Flitney.
In the 56th minute the Gills made their first change when a formation change to 4-3-3 saw Danny Kedwell
Substitute Kevin Ellison tried his luck from distance ten minutes later but his effort didn't trouble Flitney.
In the 68th minute the home side went two ahead. A crossfield ball to Reid wasn't cut out by Matt Fish
and the substitute got to the bye-line before cutting the ball back to Ellison who swept the call home just inside the far post.
Jim Bentley's side almost added a third in the 75th minute, Reid bamboozled Fish and drilled a low ball across the area which the stretching Danny Carlton miscued in front of goal.
With eleven minutes remaining Stefan Payne made it four strikers on the pitch for the Gills as he replaced Rooney.
With three minutes left Whelpdale smashed a shot goalwards which Roche parried but the flag went up before anyone could get onto the loose ball.
Then deep into stoppage time the Gills struck what proved to be little more than a consolation. Kuffour looked to be going away from goal as he moved onto a poor backpass when Roche brought the striker down with referee Carl Boyeson pointing to the spot.
After issuing a yellow card to the keeper, the only one of the game,&nbsp;and a brief argument between Kedwell, Payne and Nouble as to who was going to take it, the West Ham loanee confidently stepped up to send Roche the wrong way with virtually the last kick of the game.
The result which took Morecambe up to third place saw the Gills slip to tenth.
Morecambe: Barry Roche, Will Haining (Kieran Charnock 28), Garry Hunter, Lewis Alessandra, Chris McReady, Stewart Drummond, Gary McDonald, Laurence Wilson (Izak Reid 49), Andy Parrish, Jason Price (Kevin Ellison 62), Danny Carlton
Subs not used: Shaun Routledge, Andrew Flemming.
Gillingham: Ross Flitney, Matt Fish
, Garry Richards, Matt Lawrence, Danny Jackman, Chris Whelpdale
, Charlie Lee
, Curtis Weston (Danny Kedwell
58), Luke Rooney (Stefan Payne 79), Jo Kuffour, Frank Nouble
Subs not used: Andy Frampton
, Joe Martin
, Paulo Gazzaniga
Referee: Carl Boyeson
Assistants: Anthony Backhouse &amp; Lee Metcalfe
Fourth Official: Peter Wright