The Pilgrims were beaten 4-2 by Grantham Town at the Meres Stadium despite initial equalisers from Boughen after 15 minutes and Pratt two minutes after half-time.
The Gingerbreads took the lead for the third time with eight minutes to play and sealed their victory on the stroke of full-time to inflict United’s first defeat of the National League U19 Alliance campaign.
Boston (4-2-3-1): Oliver Swaby; Marshall Young, Jack Withers, James Gordon, Jack Brown; Jenson Bark, Jamie Gaukroger; Leighton Boughen, Harrison Holland (Leon Thornton 60), Jenson Ball (Arkadiusz Michalczyk 46); Ryan Pratt.