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Bournemouth boss Sean O'Driscoll takes over the reins at Rovers on Monday and will have his work cut out on the evidence of this display.
Caretaker manager Micky Walker made three changes to last week's winning line-up but the move backfired and there was no cohesion in the Doncaster display.
Gillingham surprised them in a lively opening and snatched the lead in the tenth minute when Andrew Crofts headed home in fine style after latching onto a great cross from Brent Sancho who cut the ball back from the byline.
Doncaster were out of luck when Jonathan Forte had an angled shot cleared off the line by Leon Johnson eight minutes later.
But the home side were not at their best and they were given another scare when Matthew Jarvis broke through to have a low shot saved in the 23rd minute.
Rovers had another escape eight minutes later when Guylain Ndumbu-Nsungu raced past Adam Lockwood to fire inches wide.
Gillingham's on-loan keeper Scott Flinders had an outstanding debut and did well to parry a shot from Paul Heffernan in the 32nd minute. Sean Thornton should have equalised when he followed up but slammed his shot wide with the goal at his mercy.
The Gills suffered a blow in the 33rd minute when defender Danny Jackman was sent off for a second bookable offence but they rocked the home side again when they made it 2-0 from the penalty spot five minutes later.
Steve Roberts was penalised for bundling over the hard-working Jarvis and Michael Flynn slammed home the spot-kick.
Flinders distinguished himself just before the interval brilliantly saving a downward header from Steve Roberts before tipping away a terrific 20-yard effort from James Coppinger.
Doncaster looked laboured and lacked the guile to break Gillingham down in the second half as the visitors sat back deep in defence.
They needed a bizarre own goal to get back into the game when an attempt at a clearance from Duncan Jupp struck team-mate Sean Clohessy in the back and unluckily rebounded into the net.
But the visitors held out to clinch three deserved points in a hectic finish.