The Pilgrims' nemesis Tom Denton and former loanee Alex Simmons both netted twice as the Shaymen secured three points, with Gregg Smith red-carded for the hosts.
Jay Rollins briefly cut the deficit with his sixth goal of the season, but United were well-beaten as their six-match unbeaten league run came to an abrupt end.
Halifax took the lead with the game’s first meaningful chance after 18 minutes. Liam Agnew slipped at the crucial moment, allowing Josh MacDonald to cross from the right and DENTON did the rest with a precise header into the bottom corner.
Chances were few and far between, with Lewis Hilliard glancing a rare header wide for the Pilgrims following Jason St Juste’s cross.
United suffered a blow on the stroke of half-time when Agnew suffered a broken metatarsal after a challenge involving former Pilgrim Scott Garner.
The Pilgrims’ afternoon took a turn for the worse 22 seconds after the break when Lincoln City loanee SIMMONS waltzed through to prod the ball beyond Dion-Curtis Henry.
Having already been cautioned before the break for his part in a melee, Smith received his marching orders in the 57th minute after leaving a foot in on Josh Wilde.
Halifax had further chances with Denton firing wide, Jordan Sinnott lifting an effort over the bar and Liam King poking off target.
United finally roused themselves, with substitute Callum Chippendale particularly prominent, and cut the deficit with a quarter of the contest to play when ROLLINS touched home Waide Fairhurst’s driven cross.
Halifax sub Richard Peniket was denied by Henry but the visitors soon restored their two-goal advantage when SIMMONS lashed home a beauty, high to Henry’s right, from 20 yards.
The final word was left to DENTON though when he sailed home a terrific curling effort from 20 yards with three minutes to play.
Boston (4-5-1): Dion-Curtis Henry; Kalern Thomas (Callum Chippendale 68), Joe Maguire, Joe Robinson, Ben Gordon; Jay Rollins, Liam Agnew (Waide Fairhurst 45), Marcus Marshall, Lewis Hilliard, Jason St Juste (George Couzens 68); Gregg Smith. Subs (not used): Courtney Wildin, Lamin Colley.
FC Halifax (4-2-3-1): Steven Drench; Cliff Moyo (Jordan Burrow 89), Scott Garner, Nathan Hotte, Josh Wilde; Liam King, David Lynch; Josh MacDonald (Jake Hibbs 82), Jordan Sinnott (Richard Peniket 73), Alex Simmons; Tom Denton. Subs (not used): Matt Brown, Tom Nicholson (gk).
Referee: Paul Graham.
Attendance: 1,236 (200 visitors).