Spartans led through Lewis McNall's 41st minute strike and looked set to take all three points despite a United performance which contained plenty of attacking football and wasted chances.
However, Duxbury headed home Shane Byrne's corner in the first minute of stoppage time to move the Pilgrims a point nearer the play-off positions with eight matches to play.
Duxbury was recalled to the starting XI, with skipper Luke Shiels missing through suspension, and Blyth's resolute defence blocked bravely from stand-in captain Tom Platt and Jordan Burrow within three minutes of kick-off.
Femi Seriki and Danny Elliott could only fire efforts off target before Marcus Dewhurst was called upon to make the first save of the game, thwarting McNall following a quick break.
Andi Thanoj saw an 18-yarder deflect narrowly wide, but it was Spartans who took the lead four minutes before half-time with McNALL slamming the loose ball home following an initial Dewhurst save.
Elliott smacked an effort against the crossbar within a minute of the restart while substitute Fraser Preston forced two saves from visiting keeper Alex Mitchell.
United finally levelled when DUXBURY powered home Byrne's corner - and the Pilgrims should have won it moments later, with Elliott heading wide from Seriki's inviting ball from the right.
Boston (3-5-2): Marcus Dewhurst; Tom Platt, Brad Nicholson, Scott Duxbury; Femi Seriki, Brad Abbott, Shane Byrne, Andi Thanoj (Fraser Preston 62), Joe Leesley (James Hanson 84); Jordan Burrow (Ntumba Massanka 76), Danny Elliott. Subs (not used): Keenan Ferguson, Ben Sault.
Blyth (4-2-3-1): Alex Mitchell; Patrick Almond, Nathan Buddle, Toby Lees, Michael Liddle; Jordan Hickey, Nicky Deverdics; Lewis McNall (Angelo Cappello 82), JJ O'Donnell, Robbie Dale (Sean Reid 67); Dan Maguire (Connor Thomson 27). Subs (not used): Karl Byrne, Corey McKeown.
Referee: Andrew Humphries.
Attendance: 1,345 (43 visitors).
PIC: Tim Hoff.