Clarke opened the scoring after just 25 minutes before Jamie Green made the points safe late on with a fine individual goal.
Rotherham made a bright start to the game and took a deserved lead when Dale Tonge’s cross eventually broke to Clarke, who lashed his shot past Simon Royce.
Nicky Southall had Gills’ first shot on target after 29 minutes and seven minutes later Simeon Jackson hit a hard low drive, but Andy Warrington saved both with little trouble.
A double substitution after 65 minutes almost paid instant dividends for Gills when Dennis Oli almost scored with his first touch. Cutting in from the left, his fierce drive cannoned off Warrington’s legs to safety.
Rotherham substitute Ryan Taylor almost added a second with ten minutes remaining before Jamie Green made sure a minute later, racing almost half the length of the field before slamming a shot into the roof of the net.