The Gills took the lead just after the 20 minute mark when a long throw from Chris Whelpdale was flicked on by Danny Kedwell for ex-Miller Burton to finish off.
Whelpdale then smashed a shot against the bar from range, and after the break Kedwell's right foot shot was also tipped onto the woodwork by keeper Scott Shearer as the Gills hit their opponents on the counter.
The Millers had alot of the ball in the second period without really threatening until the final quarter, when Alex Revell had a goalbound shot blocked by defender Matt Fish.
Keeper Stuart Nelson was then called into action as he managed to claw Michael O'Connor's thunderbolt of a volley out for a corner..
Despite that late Millers pressure, when they could also have had a penalty for a foul on Daniel Kearns in added time, the win puts the leaders a step closer to League One football next season.