Craig Midgley's late penalty secured Halfax's first points of the season.
Halifax took the lead after nine minutes at the Shay Stadium with Mark Monington firing home frin close range following a Martin Foster cross.
Boro had a Robert Gill volley ruled out for offside before Neil Redfearn levelled with a spectacular free-kick.
But with eight minutes left the home side won it with Midgley firing home from the spot after Mark Hotte had fouled Karl Munroe.
Halifax: Dunbavin, Monington, Ingram, Quinn,
Hockenhull (Howell 66), Bushell (Munroe 45), Foster, Willis, Doughty, Midgley, Sugden (Killeen 67). Subs Not Used: Mallon, Senior.
Booked: Ingram, Foster, Willis, Howell.
Goals: Monington 11, Midgley 82 (pen).
Scarborough: Walker, Lyth, Cryan, Hotte, Nicholson (Senior 88), Thompson (Foot 45), Redfearn, Kerr, Gilroy, Gill (Burton 67), Hackworth. Subs Not Used: Pounder, Gareth Downey.
Booked: Cryan, Hotte, Senior.
Goals: Redfearn 48.
Ref: M Matadar (Lancashire).