Doncaster's Dave Penney received the League One Manager of the Month award for November, but Gillingham inflicted defeat on his side thanks to a spectacular goal from Michael Flynn in the first half.
Doncaster, who have a Carling Cup quarter-final tie with Arsenal to look forward to, could argue that they deserved something out of the game and they were particularly unfortunate when substitute Jonathan Forte struck the woodwork after the break.
Gillingham opened the scoring on 18 minutes in a move which saw Matt Jarvis go sprinting past Dave Mulligan on the right before crossing low to Neil Harris.
His turn and shot was blocked which allowed Flynn to follow up and let fly with an unstoppable 18-yard shot into the roof of the net.
The lively Lewis Guy had already threatened for Doncaster with a shot wide and in the 20th minute he was off target again, this time with a header.
He was then presented with a glorious chance to put his side back on level terms on 32 minutes when Paul Heffernan rolled the ball into his path, but Jason Brown pulled off a breathtaking save to deny him from eight yards.
Three minutes later Leon Johnson sliced the ball wildly attempting to clear a Heffernan cross and substitute Paul Green was odds on to score, but Brown again came to Gillingham's rescue, clawing the ball away with one hand.
In the 67th minute Gillingham only half cleared a corner to the left hand edge of the box and Forte's powerful strike deflected on to Brown's left-hand post.
After that Gillingham closed the game out to collect all three points.