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Gillingham were left empty-handed at Barrow after conceding in stoppage-time.
An own-goal from Gillingham keeper Glenn Morris separated the sides at the break as Barrow deservedly led. The Gills improved after the break and grabbed a deserved 82nd minute equaliser as Masterson scored from a corner but substitute Robbie Gotts won it on 94 minutes.
Tristan Abrahams came in for only his second start since joining the Gills in January - replacing Oli Hawkins in the eleven. His other start came against Stockport - a match where the Gills put the defence first in a game that finished goalless.
It was Gillingham’s first visit to Barrow in over 50 years. The home side went into the weekend hanging onto play-off hopes while Neil Harris’ men - backed by over 300 fans in Cumbria - had all-but put their relegation fears behind them.
Barrow started the brighter of the teams and dominated during the opening half. Sam Foley put a shot narrowly wide with a minute on the clock.
The Bluebirds took a ninth minute lead as wing-back Tyrell Warren’s cross from the right ran to the unmarked Patrick Brough. His shot was saved by Morris but when the follow-up from Josh Gordon was cleared off the line by Max Ehmer the ball hit the goalkeeper and bounced back across the line.
It was an unfortunate goal to concede but the Gills got away with a couple of other moments, with another Waren cross causing panic as Conor Masterson could only half clear to Kay and his shot was well saved by Morris.
Gillingham were left frustrated in their attempts to break a solid Barrow defence, unable to utilise the pace of Abrahams. The Gills reached the break with just one shot at goal, Robbie McKenzie’s effort going well over the bar after a poor first half from the Kent men.
Harris made changes at the break as Cheye Alexander was switched for David Tutonda while in attack Abrahams was withdrawn as Hawkins was returned up top for the Gills.
Early on in the second half the Gills came close when Tom Nichols put an effort wide, instantly looking more of a threat. Home keeper Paul Farman also needed a defensive clearance off the line from Sam Foley to save his blushes as he missed a cross from Alex MacDonald, hitting Warren and heading goalwards, with Nichols in the mix again.
Hawkins also put a header wide from fellow substitute Tutonda.
Chances kept coming for the improved Gills side and Nichols was a fraction off converting when Tim Dieng flicked on MacDonald’s ball forward.
A rare second half chance that fell for Gordon with 15 minutes left was well saved by Morris.
Gillingham went into the latter stages still looking to test the home keeper with a shot on target. It was from their first on-target effort that they scored, with eight minutes left. MacDonald whipped in the corner and Masterson guided home a header after creating himself space inside the area.
The Gills were heading for a point but when Ben Whitfield had a shot blocked the ball ran for Gotts and he fired home from the edge of the box, beating Morris with the aid of a deflection.
Gillingham: Morris, Alexander (Tutonda 46mins), McKenzie (Wright 77mins), Ehmer, Masterson, Williams, Dieng (Lapslie 72mins), O’Brien, MacDonald, Nichols (Coleman 89mins), Abrahams (Hawkins 46mins). Sub not used: Turner.
Barrow: Farman, Brough, McClelland, Canavan, White, Neal (Whitfield 85mins), Foley (Young 85mins), Warren, Ray, Gordon, Kay (Gotts 70mins). Subs not used: Lillis, Newby, Feely.
Referee: Darren Handley
Attendance: 3,703 (320 away)