The champions, who received their Division H medals after the final whistle, prevailed courtesy of Ball’s 58th minute header from a Liam Adams cross.
Adams had earlier fired the Pilgrims in front after 21 minutes although they were pegged back eight minutes before half-time through Rhiess McLean.
Boston (4-3-3): Harry Payne; Jack Brown, James Gordon, Jack Withers, Callum Rodger; Jordan Tate, George Hobbins, Peter Evison; Jenson Ball (Jack Henton 80), Liam Adams, Haydn Havard. Subs (not used): Arkadiusz Michalczyk, Connor Stocks.