Gillingham came from behind twice before scoring a late winner to claim all three points at the Mazuma Mobile Stadium.
Jordan Slew opened the scoring on 11 minutes before Oliver Hawkins equalised seven minutes later as the score remained level at the break.
Charlie Brown fired the Shrimps ahead for the second time midway through the second half with Timothée Dieng levelling proceedings once more with just over 15 minutes of normal time to play.
Four minutes before the 90, Connor Mahoney scored the winner for the visitors.
It was a bright start from the visitors who thought they were ahead through Hawkins in the seventh minute, however the offside flag cut the celebrations short.
Slew put the Shrimps ahead after Charlie Brown won the ball down the right-hand side and drove into the middle. He then picked out the run of our number 11 who opened up his body and made no mistake, side-footing the ball into the bottom-right corner.
Seven minutes later, Hawkins got his goal at the second time of asking for Gillingham as Remeao Hutton crossed the ball into the box and, while Archie Mair was able to push away the initial danger, the rebound fell to the striker who converted from close range.
Both sides came close around the half hour mark; Dave Tutonda was played down the left before his low cross was cleared for a corner. At the other end, the Gills were awarded a free-kick to the right of goal, and Mair did well to turn the shot over the bar.
Four minutes before half time, Ged Brannan's men nearly regained their lead after Slew drove past a number of Gillingham bodies before firing a shot which nearly nestled in the top corner, but the wind carried the ball onto the roof of the net.
Half-time: Morecambe 1 Gillingham 1
The Shrimps made a bright start to the second half as Joe Adams and Slew played some lovely football down the left wing before latter's shot from the edge of the box was blocked.
Almost immediately after, Morecambe were on the attack again, forcing Gillingham's goalkeeper into a huge save as Slew looked to head the ball home from close-range.
After continuing to apply the pressure, Morecambe's persistence paid off in the 64th minute; After an initial cross found Garner, who saw a shot blocked, the loose ball fell to Brown who bundled it in at the back post.
The away side pegged Morecambe back once more nine minutes later when Dieng took aim from distance, his shot looping over Mair and finding its intended target.
With time running out, Gillingham took the lead for the first time in the game through Mahoney. His strike from the edge of the box took a wicked deflection before hitting the back of the net.
Full-time: Morecambe 2 Gillingham 3
Morecambe: Mair, Tutonda, Bedeau ©, Adams (Edwards, 76’), Garner, Senior, Slew, Stokes, Taylor, Brown (Hiwula, 89’), Khumbeni.
Subs not used: A Smith, Songo’o, Larsson, C Smith, Harrack.
Goals: Jordan Slew (11’), Brown (64’),
Bookings: Brown, Slew, Khumbeni.
Red cards: None.
Gillingham: Morris, Clark (Malone, 68’), Ehmer ©, Lapslie (Clarke,79’), Williams (Walker, 59’), Hawkins (Andrews,79’), McKenzie (Coleman, 68’), Ogie, Mahoney, Hutton, Dieng.
Subs not used: Turner, Masterson.
Goals: Hawkins (18’), Dieng (73’), Mahoney (85’).
Bookings: Malone, Coleman.
Red cards: None.
Attendance: 3,408 (208 away).
