The Pilgrims trailed to a Sean Cann goal after 32 minutes, but Miller struck on 52 and 61 minutes to fire the visitors to victory in their Ashby Avenue encounter.
Manager Dennis Greene utilised his whole squad, with the exception of goalkeeper Ashley Timms and striker Marc Newsham, with defender Scott Garner making his first United appearance 24 hours after his loan move from Cambridge United.
Boston (4-3-3): Sam Vince; Conor Marshall (Lewis Sturman 63), Scott Garner, Carl Piergianni (Stefan Galinski 46), Netan Sansara; Peter Bore (Charley Sanders 46), Ian Ross (Gary Mills 63), Ben Milnes (James Reed 72); Ben Fairclough, Spencer Weir-Daley (Jordan Nuttell 63), Ricky Miller. Sub (not used): Andy Hewitt (gk).
Referee: Gary Sutton