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Tom Eaves’ goal came too little too late for the Gills on Saturday against Luton Town.
Andrew Shinnie put Luton ahead midway through the first half and Elliot Lee struck twice in the second to put the visitors three goals infront.
Eaves’ 13th goal of the season gave the Gills hope but late pressure failed to get them back into the game.
Gills boss Steve Lovell shuffled his squad following their extra-time FA Cup win at Hartlepool in the week.
Darren Oldaker dropped to the bench while Regan Charles-Cook and Brandon Hanlan were both left out of the squad completely. Dean Parrett, Josh Rees and Elliott List all won a recall to the starting eleven.
List created an early chance for the Gills, playing in strike partner Eaves with a delicate touch, but the resultant shot went wide of the post.
Rees also sent a header wide for the Gills and Luton started to gain the upper-hand as the half progressed.
Their opening goal came in the 25th minute, struck home from the edge of the box by Shinnie, following a one-two with former Gills loanee Harry Cornick. James Collins’ movement had opened up space and Shinnie found the net past Tomas Holy.
Luton had a goal disallowed when Collins was adjudged to have shoved Barry Fuller in the back as he nodded home at the far post.
Neither team managed to create a great deal with two sides similarly set up cancelling each other out.
Chances continued to be at a premium at the start of the second half but a hopeful low cross from Collins was met by Lee, lurking between Ehmer and Luke O’Neill, and he diverted the ball into the roof of the net with 55 minutes gone to double the lead.
With an hour gone Gills boss Steve Lovell made a trio of subs in a bid to rescue something from the match.
Hopes of a fightback soon evaporated. Cornick sprinted forward from midway inside his own half, beating Darren Oldaker for pace, before striking a shot against the post. Lee was on hand to tuck the loose ball away.
The Gills had a lifeline with 18 minutes left when a crisp finish from Eaves reduced the deficit, setting himself up with his first touch before firing past the keeper for his 13th of the season.
Gillingham felt they should have had a penalty with 10 minutes left, following a handball in the box, but referee Kevin Johnson said no. Lovell appealed for another moments later after List was taken down in the area but the Gills had to make do with a corner.
The Gills were applying the pressure in the latter stages but they had too much to do in the end. Oldaker had a shot blocked, List fired wide and Eaves had headed over the bar.
Gillingham: Holy, Fuller, O’Neill, Ehmer, Zakuani, Bingham (Garmston 62mins), Byrne, Parrett (Oldaker 61mins), Rees (Parker 61mins), List, Eaves. Subs not used: Hadler, Ogilvie, Riley, Garmston, Mbo.
Luton: Shea, Justin, Bradley, Rea, Pearson, Shinnie (Sheehan 69mins), Cornick (Jarvis 84mins), Mpanzu, Stacey, Lee (Jones 90mins), Collins. Subs not used: Stech, Potts, McCormack, Grant.
Attendance: 5,671 (1,282 away)