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Substitute Aiden O’Brien scored with his first touch but Gillingham left empty-handed from promotion-chasing Northampton on Easter Monday.
It means Gills have only won once in their last eight away matches in League 2, as an improved second-half display was not rewarded in the points column.
The game pitted two of the division’s form teams against each other. Northampton were keen to respond from a Good Friday reverse at Doncaster while the Gills – almost perfect at Priestfield since the turn of the year - wanted away points on the board.
Neil Harris made three changes for Gillingham from the team that beat Doncaster on Good Friday.
In come Will Wright, Dom Jefferies and George Lapslie for Alex MacDonald, O'Brien and Conor Masterson, who came off in that game with a head injury.
The game also marked a 350th Gills appearance for defender Max Ehmer while former Gills youngster Harvey Lintott was among a three-man Northampton defence.
Former Dover man Mitch Pinnock sent a second-minute shot well wide for the hosts but it was a largely quiet opening period as Gills’ 4-4-2 came up against the hosts’ favoured 3-5-2 formation.
Pinnock’s cross was headed wide by Louis Appere under pressure and skipper Jon Guthrie headed over from a Pinnock corner.
Gills never had a shot at goal in the first half, their best opening came on 25 minutes when Guthrie had to clear the ball from the feet of Tom Nichols after strike partner Oli Hawkins headed a Robbie McKenzie centre into his path.
Northampton’s attacks started to gather momentum – McKenzie did well to block a Sam Hoskins drive – so it was no surprise when they took a 32nd-minute lead. Pinnock’s cross from the right was tentatively headed clear by Wright into the path of Appere, who finished in style beyond keeper Glenn Morris.
It needed a fine save from the veteran Gills keeper five minutes later to deny Northampton a second goal. The visitors were caught napping from a short corner, and Marc Leonard had time and space to deliver into the area where Guthrie’s downward header was pushed out low down by Morris.
Gills replaced Jefferies with Lewis Page for the second half, also changing formation to match up to the hosts’ 3-5-2.
While it meant there was less threat from the hosts, Gills still needed more going forward so Harris made a triple change just past the hour mark.
It had an instant impact as confusion in the home defence saw the ball fall for Hawkins and his cross-shot into the danger area was turned in at close range by the sliding O’Brien with his first touch.
Referee Darren Drysdale took an age to eventually book defender David Norman for an awful challenge from behind on Nichols with 20 minutes left.
O’Brien took advantage of a fortunate bounce on the edge of the box before firing just wide of the upright with keeper Lee Burge beaten and it was an increasingly nervous atmosphere among the home fans as the Gills started to ask more questions.
But then the game swung back in Northampton’s favour with a moment of magic from midfielder Will Hondermarck, who brilliantly picked his spot from 25 yards to give the home side the lead with just eight minutes left.
Gills nearly snatched a last-gasp leveller but Nichols headed wide from a MacDonald free-kick in the fifth minute of stoppages.
Northampton: Burge, Guthrie, Hoskins, Appere (Hylton 77mins), Pinnock, Leonard, Norman, Hondermarck, Bowie (Yengi 88mins), Lintott (Sowerby 46mins), Haynes. Subs not used: Wright-Phillips, Tomlinson, Osew, King.
Gillingham: Morris, Alexander (MacDonald 62mins), Wright (Abrahams 88mins), Ehmer, Williams, McKenzie, Jefferies (Page 46mins), Nichols, Hawkins, Dieng (Coleman 62mins), Lapslie (O’Brien 62mins). Subs not used: Tutonda, Holtam.
Referee: Darren Drysdale.
Attendance: 6,904 (847 away).