United fielded a host of new faces and trialists at The Jakemans Stadium and led through Thewlis' 49th minute penalty.
Matt Green equalised for Town on 64 minutes but United's trialist right-back sailed home a beauty from 30 yards with four minutes remaining to win it for the Pilgrims.
Boston (4-3-3): Peter Crook (George Willis 58); Ben Middleton, Luke Shiels (Trialist A 58), Simon Ainge (Trialist C 58), Ashley Jackson (Alex Whittle 58); Brad Abbott (George Green 58), Andi Thanoj (Trialist B 58), Tom Platt; Jay Rollins, Tom Clare, Jordan Thewlis (Jonathan Wafula 58). Subs (not used): Dominic Knowles, Nicky Walker.
Referee: Kevin Friend.
Attendance: 682 (262 visitors).