The Pilgrims dominated the first half at Skegness Sports Association but fell behind to a penalty on the hour mark.
Halifax doubled their lead shortly afterwards and subsequently held off United's attempts of a fightback, as both Xander Crashley and Daniel Fisher went off injured.
Boston (3-5-2): Jake Frestle; Brogan Horniman, Harry Cranfield, Daniel Fisher (Jack Bastow 59); Joe Hardstaff, Jamie Gaukroger, Finlay Armond, Will Jackson, Nathan Stevens; Tom Wilkinson, Xander Crashley (Ashton Taylor 40). Sub (not used): Craig Forbes.
Referee: Ian Ruddock.