The Pilgrims were beaten by a terrific long-range strike in first half stoppage time and a second 10 minutes after the break at a soggy Jakemans Stadium.
Lee Mitchell's side were unable to force a route back into proceedings after seeing a string of chances go begging before the break.
Boston (4-1-4-1): Nick Ivanov; Jamie Gaukroger, Harry Cranfield, Daniel Fisher, Nathan Stevens; Marshall Young; Xander Crashley (Elliott Ramsden 67), Mido Turki, Jenson Bark, Will Jackson; Harrison Holland. Subs (not used): Cole Willerton, Marc Tucker.