Bradford had dominated for much of the game, but Gills boss Justin Edinburgh rang the changes in the second half and was rewarded with a sweet curling effort from Marquis, which sealed a 1-0 win.
Bradford had the upper hand in the first half, using James Hanson and Jon Stead’s height to their advantage, and nearly reaped the rewards from a corner as the latter saw his goal-bound header cleared off the line.
The visitors went agonisingly close to taking the lead from a corner minutes before the break, but Glenn Morris made two close-range saves from Stead and Hanson.
Gillingham should have taken the lead midway through the second period, but Cody McDonald hesitated with the goal at his mercy having been teed-up by Jermaine McGlashan, and saw his effort closed down by defender Gary MacKenzie.
But the Gills eventually made the most of an increasingly stretched game as substitute Marquis found space and curled the ball past visiting goalkeeper Ben Williams in the 72nd minute.
Bradford skipper Stephen Darby then cleared off the line late on to prevent Marquis from doubling his tally.