Goals from Bradley Dack and Deji Oshilaja secured the points for the hosts.
Dack opened the scoring after seven minutes, but despite a dominant second half showing from Dale, Oshilaja doubled the Gills’s advantage ten minutes from time.
Manager Keith Hill made two changes to the side that lined up against Doncaster Rovers on Saturday.
Joe Rafferty returned from injury to replace Peter Vincenti, while Calvin Andrew came in for Joe Bunney.
After an even start to the game, the hosts opened the scoring after seven minutes through Bradley Dack.
A foul on Donal McDermott just outside the Gills' 18-yard box went unpunished and the home-side hit Dale on the break. Dack stormed at goal from midfield and a sent a fine finish beyond the Joel Castro Pereira.
Rochdale’s best opportunity of the half came in the 37th minute when Ian Henderson got to the byline before cutting the ball back for Cannon, who had an effort saved by Stuart Nelson at his near post.
Shortly before half time, Rochdale were awarded a free-kick after Rhys Bennett was upended as he attempted to break into the area.
McDermott took the set-piece, which was just a few yards from the byline, and forced the goalkeeper into a save, beating away the free-kick.
HT: GILLINGHAM 1-0 ROCHDALE
Manager Keith Hill made his first substitution of the game at the interval, as Nathaniel Mendez-Laing replaced Rafferty for the start of the second half.
Dale looked to playing with more of an urgency and three minutes after the re-start McDermott dragged an effort wide of the upright.
Tom Kennedy then saw an effort go over the bar, before James Hooper was introduced to make his first team debut.
Hooper, an Academy graduate, who signed his first professional contract in the summer, replaced McDermott with 52 minutes on the clock.
After the change, Gillingham’s Rory Donnelly sent an effort into the hands of Castro Pereira.
Dale’s third and final substitution came in the 65th minute when Kennedy made way for Michael Rose.
Two minutes later, and Nelson was forced to palm away an effort from Andrew, which was struck from distance.
Dale were on top and continued to apply the pressure.
A Rose free-kick, 22-yards from goal, left Nelson rooted to the spot, but agonisingly, the set-piece travelled narrowly wide of the upright.
Hooper was then denied by a fine save from the goalkeeper, who stretched the length of his goal to turn a powerful shot from the youngster round the post.
Up the other end, Castro Pereira kept out Dack, whose effort from 25-yards looked headed for the top corner of the net. The on loan Manchester United stopper flew across his goal, getting two hands behind the effort.
Dale had been excellent throughout the half but were dealt a blow with ten minutes of the game remaining as Deji Oshilaja doubled the hosts’ advantage.
Rochdale continued in search of a goal but the Gills defended resolutely to claim the points.
FT: GILLINGHAM 2-0 ROCHDALE