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For the second time in a week the Gills were denied a seemingly clear goal by the match officials.
Plymouth added to their pain by clinching a last-minute winner.
The hosts had Joel Grant’s opener cancelled out by Tom Eaves – the man who was denied a seemingly clear goal after 13 minutes - but Toumani Diagouraga struck in the final minute.
Gillingham had also been denied a certain goal when Josh Parker’s midweek effort crossed the line against Oxford.
The Gills went into the match unbeaten away from home in the league, under manager Steve Lovell, winning three and drawing one.
Just three points separated the two teams, Argyle starting the weekend sitting bottom of the League 1 table.
Ben Nugent was chosen to partner Max Ehmer in the centre of Gills’ defence, with boss Steve Lovell leaving regular starter Gabriel Zakuani on the bench.
Striker Conor Wilkinson missed out through injury.
Plymouth debutant keeper Kelle Roos – their seventh different person to play in goal this season – had a let-off early on when he allowed Eaves’ shot to slip through his grasp. It looked to have crossed the line before Roos scrambled back to save but the officials waved play-on.
Neither keeper was overly tested in the half after that, with the Gills failing to make the most of numerous corner kicks.
Plymouth wide-man Grant had a shot saved and so did Gary Sawyer but neither were good enough to severely worry Gills keeper Tomas Holy.
Graham Carey went close early in the second half for the hosts, his deflected shot landing on the roof of the net, before the subsequent corner was headed wide.
Grant gave Plymouth a 56 minute lead, showing persistence in the box to get past Luke O’Neill, then driving a low shot through the legs of Ehmer and past keeper Holy.
The Gills were restricted to half-chances themselves, as they looked for a way back in. Parker had a weak shot saved and looped another shot over from distance, but Grant remained a threat at the other end, teasing the defence before firing just over from inside the area.
Gillingham’s corner count was in double figures but they struggled to test the keeper. Lovell sacrificed a defender in Connor Ogilvie in the latter stages, introducing Elliott List with 13 minutes left.
The Gills claimed a deserved goal on 87 minutes when Eaves latched onto a ball from deep before gently lifting it over keeper Roos to notch his ninth of the season.
But it wasn’t enough to bag the Gills a point as Diagouraga hit home, miss-cuing his first effort, to leave Nugent in no-man’s land and then side-footing home at the second attempt.
Gillingham: Holy, O’Neill, Ogilvie (List 77mins), Nugent, Ehmer, Clare, Byrne, Wagstaff, Martin, Eaves, Parker. Subs not used: Nelson, Lacey, Hessenthaler, Zakuani, Oldaker, Cundle.
Plymouth: Roos, Sawyer, Edwards, Carey, Jervis, Bradley, Grant (Songo’o 77mins), Taylor-Sinclair, Taylor, Fox, Diagouraga. Subs not used: Cooper, Miller, Ainsworth, Blissett, Threkeld, Wylde.
Attendance: 11,155 (398 away)