Cody McDonald's 25th goal of the season, an 88th minute header, finally broke through Morecambe's resilient rearguard.
The Gills had plenty of chances as they pushed the visitors deeper and deeper but on the occasions they did get through they found keeper Barry Roche was in fine form.
That point gained can still prove vital though as the race for promotion continues whether it be automatic, which is beginning to look a little doubtful now, or via the play-offs.
Andy Hessenthaler's side remain seventh in the table, one of four clubs on 65 points, but are now five points behind Wycombe Wanderers who currently hold the third automatic spot.
With Curtis Weston coming through a fitness test on his knee, boss Hessenthaler named the same starting XI that had begun the 4-0 thrashing of Lincoln City last Saturday. Mark Bentley who has returned from his loan spell at Cambridge United was included on the bench.
The Gills survived an early scare in the third minute, Garry Hunter knocked a free-kick forward, Will Haining headed on but Phil Jevons didn't connect cleanly from six yards out allowing Alan Julian to save comfortably.
In the eighth minute Barry Fuller got forward from right-back, cut inside two defenders but saw his stinging left-footer beaten away by keeper Roche.
A great ball forward from Matt Lawrence sent Andy Barcham down the left but his pull-back saw Danny Spiller have a shot blocked.
Danny Carlton was booked in the 18th minute following a tussle with Fuller on the touch-line.
Just a minute later and people were left scratching their heads as referee Danny McDermid pointed to the spot after Jevons and Lawrence had challenged for the ball to the left of Julians goal. He also booked the Gillingham defender although it was unclear from up in the press-box as to what for. I don't think we were the only ones who didn't know though judging by the cat-calls from around Priestfield.
However Jevons kept his cool in front of the Rainham End and stepped up to send Julian the wrong way from the resultant spot-kick.
Morecambe, who have a decent away record, had obviously done their homework rather like Hereford in the previous home game , they often put two players on Akinfenwa and Barcham, which didn't help the Gills from a creativity point of view. They were also slowing things down at every opportunity.
The Shrimps nearly went two-up on the half-hour, Niall Cowperthwaite crossed from the left and the ball broke invitingly for Carlton to volley a low shot which Julian clutched.
A great move in the 37th minute almost saw the Gills level matters. A grounded Spiller touched the ball to Weston, he played the ball forward to Adebayo Akinfenwa who in turn laid it off for Kevin Maher to crack a shot goalwards from around 25-yards which Roche again beat out.
The Gills continued to press for an equaliser, a low Fuller cross was half-cleared to Barcham but his low strike was deflected wide. Then Akinfenwa saw his goalbound header force Roche to claw out low to his right and then McDonald raced through but his shot was straight at the former Nottingham Forest keeper.
H/T: 0 - 1
Shortly after Kevan Hurst had headed a good chance over, the Gills made a double substitution. John Nutter replaced a limping Joe Martin while Luke Rooney took over from Maher. Spiller moved into a central position with Rooney going right.
I'm not sure whether it was the changes but the Gills suddenly began to create more and more openings.
First McDonald cut inside from the left and drilled a low shot goalwards which Roche turned aside then Fuller burst forward onto a Rooney pass and crossed, Barcham headed back across goal where McDonald forced another decent save from the keeper, diving to his left, with an overhead kick.
Stewart Drummond became the second Morecambe booking for tugging back Barcham in the 66th minute and he was quickly followed by keeper Roche for time-wasting.
The Gills third change saw Jack Payne take the place of Weston.
With the Gills well in the ascendancy, Akinfenwa set up a great shooting chance for Spiller but the midfielder side-footed straight at the keeper.
Spiller then ran onto a Lawrence pass but Roche saved with his feet at the near post and soon afterwards Rooney put a long range shot just off target.
The visitors switched to 4-5-1 when making their third change of the afternoon in the 75th minute, taking off Jevons with Scott Brown being introduced.
Just when it seemed that the Gills weren't going to make a breakthrough that their pressure deserved they finally did in the 88th minute.
Nutter got to the left goal-line and crossed deep where McDonald rose to plant a header back across Roche and into the far side of the net. Priestfield erupted - well everyone except the 68 Morecambe fans anyway.
There was nearly as big a cheer when the five minutes of time added-on was shown as the Gills went in search of a winner.
Barcham cut in from the left and drilled a shot across the face of goal, which a defender did well not to get a touch to.
Then a crunching tackle on Fuller earned Cowperthwaite the visitors their fourth booking, and it almost proved even more costly.
Nutter played the free-kick in and there was an almighty goalmouth scramble as a number of Gills attempted to get a clear shot or header while the Shrimps defended for their lives, the ball eventually finding its way to Barcham who fired a left-foot effort wide.
The Gills had certainly given it there all but they only managed to breach the Morecambe defence, which dropped further and further back, the once.
Gillingham: Julian, Fuller, Gowling, Lawrence, Martin (Nutter 58), Spiller, Weston (J.Payne 69), Maher (Rooney 58), Barcham, McDonald, Akinfenwa.
Unused subs: Cronin, Richards, Bentley, Jackman .
Morecambe: Roche, McCready, Haining, Parrish, Cowperthwaite, Holdsworth, Hurst (Wainwright 73), Drummond, Jevons (Brown 75), Hunter, Carlton (Spencer 64).
Unused subs: Shuker, Walker, Bentley, Aley.
Attendance: 5545 (68 Morecambe)
Referee: Danny McDermid
Assistants: Wes Linden and Rob MacKay
Fourth Official: Nick Kinseley