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Josh Parker bagged a point for the Gills with a late goal at Priestfield.
Neil Danns had put second from bottom Bury a goal ahead at the break in Saturday’s League 1 drop-zone scrap.
Andrew Tutte hit the woodwork in the second half for the visitors, who would have leapfrogged Gills with a win, but with five minutes left Parker headed home a Lee Martin corner to level the scores.
Gillingham made just one change from the previous week’s FA Cup win over Leyton Orient, with Luke O’Neill replacing Gabriel Zakuani.
It was Steve Lovell’s seventh senior game in charge of his interim spell, hoping for the win that could have lifted them out of the League 1 drop zone.
Reaction: It was a massive point, says the caretaker boss
Opponents Bury sat a place behind them in the table and the Gills were eager to get one over a relegation rival, having recently lost out to fellow strugglers Northampton at home. That was Lovell’s only defeat of his caretaker spell.
Bury, who were targeting promotion at the start of the season, sacked manager Lee Clark recently and it was Ryan Lowe’s first league game at the helm after being put in temporary charge.
The Gills got themselves into some good positions early on but their final ball let Bury off the hook.
Lovell had started the match with a 4-5-1 formation but switched to three at the back midway through the half as the pressure from Bury intensified.
The visitors went close through Nicky Ajose and took the lead six minutes before the break. Eoghan O’Connell spotted the run of Danns and fed the forward, who then drilled home low past Tomas Holy.
Michael Smith put a great chance wide moments later, shooting wide from infront of goal off an Ajose cross.
Conor Wilkinson joined Eaves up top for the second half and fired an early chance high and wide. Parker went closer from a corner but couldn’t keep the shot down.
Ajose went close for the visitors with an hour gone while Parker and Eaves both tested the reactions of Italian keeper Fasan. Mark Byrne scuffed a shot agonisingly wide with 20 minutes left after Holy’s long clearance put Bury under pressure.
Wilkinson blasted another chance wide for Gills after his chased Eaves’ flick-on but it was Bury who came closest, a curling shot from sub Tutte bouncing off the upright after beating Holy.
Clare stung the hands of Fasan with 10 minutes left and Martin then fired over after retrieving the loose ball.
Gillingham’s desperation meant they were open at the back and Ajose nearly capitalised, lashing a shot at goal, denied only by a strong hand from Holy.
The Gills kept the pressure on and were rewarded when Parker met Martin’s corner and powered his header down past Fasan.
Gillingham: Holy, Clare, Ogilvie, O’Neill, Ehmer, Byrne, Hessenthaler, Parker, Martin, List (Wilkinson 46mins), Eaves. Subs not used: Nelson, Simpson, Wagstaff, Chapman, Oldaker, Cundle.
Bury: Fasan, Leigh, O’Connell, Ajose, Williams, Edwards, Aldred, O’Shea (Reilly 88mins), Smith, Ince, Danns (Tutte 68mins). Subs not used: Maguire, Humphrey, Whitmore, Sang, Moloney.
Attendance: 4,364 (141 away)