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Gillingham put their cup disappointment behind them with a table-topping win at Priestfield.
Debutant Dominic Samuel took just six minutes to open his account for the Gills after cancelling out Leon Clarke’s early opener.
John Egan completed a frantic first 10 minutes by putting the Gills ahead.
A super goal late on from Emmanuel Osadebe wrapped up the points.
The Gills knew victory could take them top of the league, depending on Coventry’s result at Colchester, as the leading pair Walsall and Burton weren’t in action.
A 3-1 win was enough to return to the League 1 summit.
Justin Edinburgh’s side were back in league action and looking to put defeats in the FA Cup and Johnstone’s Paint Trophy behind them.
There were three changes to the Gillingham starting XI, with captain Doug Loft dropped in favour of Jake Hessenthaler.
New loan signing Samuel started upfront alongside Rory Donnelly as Cody McDonald dropped out of the XI.
Bury started the afternoon sitting sixth in the table but had keeper problems, which meant they named an 18-year-old debutant in goal. They also had just four substitutes.
The visiting keeper Jack Ruddy was beaten twice in the opening 10 minutes as the Gills quickly overcame a goal deficit.
The game was just four minutes old when Bury’s Leon Clarke headed home Danny Mayor’s cross. The visitors attacked after Emmanuel Osadebe had lost possession for the hosts.
But just two minutes later the Gills were level. Bradley Dack’s free-kick hit the wall and fell to Hessenthaler, his effort took a deflection and found Samuel, who made no mistake from close-range.
The Gills then went ahead from another free-kick. Bradley Garmston whipped the ball in, it was headed into the path of Egan and he stabbed home to make it 2-1.
Gillingham had chances to go further infront, as Osadebe had a shot deflected over and Dack fired a free-kick over, while Donnelly should have done better with the delivery when breaking clear on the right.
Bury had their own chances but the Gills kept hold of their lead by the break. Josh Wright tested keeper Ruddy with a stabbed effort in the opening stages of the second half while Osadebe found the top of the Rainham End with his wild shot.
With an hour played it took a great tackle from Garmston to deny Bury sub Danny Rose and Leon Clarke put a header from the subsequent corner wide. The visitors went close again moments later, with a Rose header cleared off the line by Harry Lennon.
The change around in attack helped Bury put some pressure on but Samuel came close to a Gills third, driving a low shot that Ruddy had to get down to save.
The best goal came from Osadebe. With 87 minutes gone he surged forward from the halfway line, played a one-two with a defender and then nutmegged another before curling the ball past the keeper with the outside of his foot.
Osadabe turned defender moments later, heading bravely off the line in a crowded area, as Tom Pope looked to pounce. Ryan Jackson also had to head a dangerous ball clear in stoppage-time.
Gillingham: Nelson, Jackson, Garmston, Egan (Oshilaja 90mins), Lennon, Wright (A Morris 86mins), Hessenthaler, Osadebe, Dack, Samuel (McDonald 86mins), Donnelly. Subs not used: G Morris, Loft, McGlashan, Dickenson.
Bury: Ruddy, Riley, Hussey, P Clarke, Cameron, Pugh (Rose 60mins), Mayor, Soares, Mellis (Brown 78mins), L Clarke, Pope. Subs not used: Sedgwick, Burgess.
Attendance: 6,063 (212 away)