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The Gills notched up their first away victory since August with a rare double after beating Wigan at home last week.
Rotherham, with only one home victory this season, started brightly and might have edged in front.
Martin Butler burst through after a clever ball from Paul Warne but was shut out by impressive defensive work.
Then Warne cut inside from the right and lashed a 20-yard effort that was well saved.
Stan Ternent's side then went ahead against the run of play with a Michael Flynn goal in the 26th minute after neat ball from Paul Smith.
It gave Gillingham the boost they wanted and they could have gone further in front at half time.
Marli international Mamady Sidibe found space and charged through but keeper Mike Pollitt raced out and cleared.
Gillingham might have increased their lead early in the second half but Nicky Southall hit the post with a blistering effort.
In the 66th minute Butler levelled for Rotherham when the ball broke kindly for him and he smashed a low shot past the keeper.
Gillingham regained the upper hand in the 72nd minute when Sidibe muscled his way past Phil Gilchrist and hit his shot past Pollitt.
Eight minutes from the end Sidibe was involved again as he produced an impressive ball for Darius Henderson to complete the scoring.