Goals in each half from Morten Bisgaard and Paul Peschisolido were enough to seal a well organised Gillingham side who failed to take their chances.
The finishing was the difference between the teams as Derby accepted the openings that came their way while the visitors squandered theirs.
Darius Henderson and Darren Byfield both wasted one on ones with Derby goal keeper Lee Camp either side of Bisgaard's 33rd minute opener.
Camp was also outstanding on a day when a strong swirling wind made conditions awkward and his growing confidence has been one of the reasons behind Derby's advance towards a top-six finish.
Gillingham were unbeaten in nine before this and showed why with a solid display that suggests they would get the point they need to stay up.
On another day, Henderson and Byfield would surely have scored but instead manager Stan Ternent was left holding his head in frustration.
Bisgaard showed how it should be done when he swivelled to volley past Jason Brown from 12 yards after Chris Hope had sliced his attempted clearance.
Gillingham should have cancelled that goal out at the start of the second half when Nicky Southall crossed to the back post were Jon Douglas saw his close-range shot brilliantly saved by Camp.
Derby put the game out of Gillingham reach in the 72 minute when Grzegorz Rasiak went through the middle and although Brown blocked his low drive, the ball fell kindly to Peschisolido who flipped it into the empty net.