Joe Simpson's Pilgrims conceded twice within the final 10 minutes to spurn the chance of a first league double in their favour.
The National League U19 Alliance Division F encounter was played on the main pitch at the Jakemans Community Stadium.
Boston: Austin Barker, Finley Hipkin, Alex Van-Tam (Charles Doble 83), Leon Hagger (Finley Mackey 66), Dominic Chew (Kye Rook 85), Kirill Snikeris, Toby Cotton, Zac Hardy, Rhys Smaller (Louie Wain 60), Jesse Ward, Will Pettitt.
Referee: Trevor Basker.