Josh Kelly's first-half proved decisive for the hosts, who had also beaten Chesterfield at York Road on Tuesday night.
It was a subdued, well-below-par performance from Town, who will need to be much better against Boreham Wood on Tuesday.
Maidenhead had the hunger and aggression that has helped propel Halifax into the promotion race this season, and The Shaymen could have no arguments about the result.
Sam Johnson missed a league game for The Shaymen for the first time in more than four years, with illness meaning he and Jordan Slew dropped out.
Tom Scott made his first competitive appearance for Halifax, barring West Riding County Cup games, in a side which saw Martin Woods replace Kian Spence and Jay Benn start on the right wing.
It was nothing short of a dominant start by Town, who completely controlled the game's early stages, producing composed, assured and purposeful possession.
Matty Warburton brought a save from Dan Gyollai seven minutes in with a bobbly shot across goal following a flowing move down the left that was typical of Town's opening 10-minute spell.
But the hosts weathered it and grew into the contest. Charlee Adams blasted a shot way over the bar from 20 yards before a poor headed clearance led to a shot straight at Scott in the Town goal.
Kieran Green, who'd started as well as anyone for Town, was then forced off injured midway through the first-half, replaced by Jesse Debrah - surprisingly rather than the presumably unfit Spence or Luke Summerfield - with Niall Maher moving to midfield as The Shaymen's unfamiliar look continued.
It went from bad to worse when Halifax lost possession in midfield and were left exposed at the back, with dangerman Kelly producing the precise low finish of a striker in form across goal from an angle.
Kelly, who netted twice against Chesterfield in midweek and twice at The Shay in November, then turned Tom Bradbury inside out before blasting a shot just over from the corner of the six-yard box.
Halifax's joie de vivre of earlier had deserted them. Maidenhead were now the superior side.
The Shaymen were missing the drive and energy of Green and Spence in midfield, while Billy Waters was unable to influence play as much as normal on the left flank.
Emile Acquah went within inches of heading Maidenhead further in-front shortly before half-time, which Halifax looked like they badly needed.
Town had become increasingly lightweight as the half went on, too passive, too easy to play against and too easy to defend against.
All of which was all the more mystifying given how well Pete Wild's men had started the game. But they'd been second best since then.
There was more shuffling around as Harvey Gilmour replaced Warren, with Benn going to right-back, Jamie Allen to right-wing and Waters through the middle.
Remy Clerima should have done better when he was found in space a few yards out just after the restart, miscuing his shot.
Warburton should have done better too when he ballooned a shot over from 20 yards after being teed up by Allen.
Kelly again went close when he headed a volleyed cross just wide, with he and Acquah proving too strong and quick to handle for Town's under-pressure defence.
The Shaymen were nowhere near as effective as Maidenhead going forward, possessing none of their usual intricate, incisive build-up play.
The Shaymen had scored seven the last time they'd met Maidenhead, but one looked beyond them here.
Halifax switched to 3-5-2 in an attempt to find a foothold in the game, but Maidenhead remained the better side, with the excellent Acquah setting up Kelly, who dragged a shot wide.
Maidenhead keeper Dan Guollai remained underworked, with Town seeing plenty of the ball but rarely venturing inside the hosts' penalty area.
The Shaymen put some dangerous crosses through the Maidenhead box as the clock ticked down, ending the contest as dominant as they'd started it.
But an equaliser was beyond them.
Maidenhead: Gyollai, Sheckleford, Massey, De Havilland, Beckwith, Wells (Smile 88), Clerima, Adams, Upward, Acquah, Kelly (Smith 82). Subs not used: Palmer, Parry, Donnellan.
Scorer: Kelly (29)
Shots on target: 5
Shots off target: 12
Halifax: Scott; Warren (Gilmour 46), Benn, Maher, Bradbury, Senior; Green (Debrah 25), Woods, Warburton; Allen, Waters. Subs not used: Summerfield, Swaby-Neavin, Spence.
Shots on target: 1
Shots off target: 8
Referee: Robert Whitton
Town man of the match: Few to choose from. Jack Senior was probably as good as anyone in purple, showing plenty of energy down the left.