The Pilgrims led 2-1 at half-time, courtesy of goals from Cody Elgie and Stephen Pereira.
A red card for Elgie at 2-2 in the second half ultimately tipped the balance in the visitors' favour.
Boston: Joe Douce, Harry Gunthorpe (Jaydon Sargent 86), Alex Van-Tam, Kye Rook (Daniel Walsh 86), Joel Smith, Ashley Carroll, Cody Elgie, Charles Doble, Stephen Pereira (Harley Stanton 86), Matas Gecas, Kiaran Grove. Subs (not used): Finley McDaid, Tyler Griffin (gk).
Referee: Peter Brothwell.