The Pilgrims conceded from a hotly-disputed spot-kick in stoppage time to lose 3-2 - having led 2-1 at half-time.
Krisztian Gagyi had bagged a first half brace - but United conceded twice after the break to surrender their winning position.
Boston (3-4-1-2): Oliver Ford; Taylor Jaine, Owen Sheriff, Ben Robson; Krisztian Gagyi, Finlay Armond, Mackenzie Burdass, Zane Millar; Han Stevens, Ben Johnson; Elliot Foster. Subs (used): Sam Harris, Logan Tate, Jack Waddington.
Referee: Michael Bonage.