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Substitute Jake Hessenthaler struck Gillingham’s winner on Saturday.
His second-half strike was too powerful for defender Mitchell Lund to keep out as he tried to make a block on the line.
Doncaster were wasteful in front of goal and the Gills did just enough to take maximum points. The win took them back to the top of League 1.
There were a number of surprises in the Gills line-up, with three of the regular back four missing. John Egan, Deji Oshilaja and Brennan Dickenson were all out, having been fit and available in the middle of the week.
Manager Justin Edinburgh’s reaction, including news on the team changes, to follow shortly.
Captain Doug Loft returned to make his first start and Cody McDonald was also in the starting XI for the first time this season. Hessenthaler and Rory Donnelly both dropped to the bench.
Gillingham bossed the opening stages of the first half but failed to test visiting keeper Thorsten Stuckmann.
Emmanuel Osadebe had a long-range effort and Bradley Dack clipped one in but Stuckmann claimed them both.
Doncaster took some time to warm up, not having their first real shot on target until late in the half, and the Gills were thankful for some poor finishing from striker Curtis Main.
He had already put a good effort wide before the ball dropped to him in the box. Gills keeper Stuart Nelson came to the rescue, racing out to block the shot.
Just before the break Oscar Gobern put an effort into the side netting for the visitors.
Doncaster had justifiable appeals for a penalty early in the second half. Cedric Evina took the ball past Ryan Jackson but tripped on the way through. Referee Christopher Sargison said play on, amid big appeals from the visitors.
Main let the Gills off again in when the ball squirmed through to Main, through Josh Wright’s legs, but the striker shot wide.
Wright, having a busy and productive game in the middle, came close for the Gills. His ball into the box evaded everyone and crept just past the far post.
Osadebe had a shot and then a glancing header at goal but neither effort troubled Stuckmann.
The Gills took the lead on 66 minutes and had assistant referee Gavin Muge to thank. Hessenthaler drove a powerful effort at goal, it was blocked by Lund, but the eagle-eyed official spotted it had crossed the line and the hosts were ahead.
Luke Norris had a long-range volley palmed away by the keeper while at the other end Cameron Stewart smashed a shot well wide after Lund’s great cross picked him out at the far post.
Gillingham: Nelson, Jackson, Garmston, Ehmer, Houghton (Hessenthaler 60mins), Wright, Loft, Osadebe, Dack, Norris (Donnelly 90mins), McDonald (Williamson 74mins). Subs: McGlashan, G Morris, M Dickenson, List.
Doncaster: Stuckmann, Lund, Taylor-Sinclair, Butler, MacKenzie, Evina (Stewart 70mins), Coppinger, Gobern, Chaplow, Main (N'Guessan 70mins), Williams. Subs: Marosi, Keegan, P.McKay, Middleton, Whitehouse.
Attendance: 5,685 (234 away)