The Pilgrims shared the spoils at The Shay by holding their play-off chasing hosts.
Alex Simmons came closest for the Pilgrims in the opening minute, with teenager Harry Vince excelling on his full debut in United colours.
United boss Adam Murray had opted to make four changes ahead of kick-off, with Vince among those coming into the side.
Simmons linked up well with Colby Bishop inside the opening seconds but crashed his effort on to the roof of Sam Johnson’s net via a large deflection.
Halifax had started as firm favourites but United keeper Ross Durrant was on hand to repel long-range free-kicks from Matty Kosylo and Richard Peniket during a tight first half.
Durrant saved with his legs to deny Peniket after half-time before producing a fine stop to keep out Matt Brown’s header from a Jordan Sinnott free-kick.
United’s best effort of the second period fell to Bishop, but his drive was deflected into Johnson’s arms by a terrific recovering challenge from Brown.
FC Halifax (4-4-2): Sam Johnson; Kevin Roberts, Scott Garner, Matt Brown, Josh Wilde (Cliff Moyo 81); Matty Kosylo, David Lynch, Liam King, Danny Clarke (Jordan Sinnott 73); Richard Peniket, Adam Morgan (Tom Denton 46). Subs (not used): Nathan Hotte, Steven Drench (gk).
Boston (4-5-1): Ross Durrant; Kalern Thomas, Josh Robinson, Tom Batchelor, Jan Yeomans; Alex Simmons, Harry Vince, Adam Chapman, Lewis Hilliard (Callum Chippendale 90), Ben Gordon; Colby Bishop (Marcus Marshall 86). Subs (not used): Shane Clarke, Joe Fitzpatrick, Joe Maguire.
Referee: David McNamara.
Attendance: 1,752 (84 visitors).