Harker equalised after Lucas Weaver's opener, but Aaron Turner's late goal earned Colne the win.
A Matty Warburton penalty and two goals from Mani Dierseruvwe had earned a different Halifax side a 3-0 win at Curzon Ashton at lunchtime.
Angelo Capello had a shot beaten away by the Colne keeper a few minutes in after he nicked the ball high up the pitch and drove towards the box.
But the hosts took the lead shortly afterwards when they stole possession near the edge of the Halifax box, catching Festus Arthur on the ball, and Weaver swept a neat finish beyond the reach of Tom Scott.
Only a good block by Town's triallist left-back then prevented Jack Doherty's shot reaching the target, with Halifax looking shaky at the back.
Milli Alli fired narrowly wide, cutting in from the left on his right foot, with Town looking a threat when they found the time and space to play.
The Shaymen were showing better quality on the ball but Colne were aggressive, not letting Halifax settle.
Striker Harker competed well in the air against two uncompromising Colne centre-backs but didn't see much of the ball at his feet.
When he did, he produced a clever first time shot from Alli's cross, which would have gone in had it not been straight at the keeper.
Former Colne man Jamie Cooke also fired straight at the stopper after a one-two with Alli.
Halifax then hit the post with a header from a corner, before having two shots blocked in the aftermath.
An equaliser seemed to be coming, and duly arrived ten minutes before the break when Capello did well to find some space and feed the onrushing Jack Hunter, who then cleverly played in Harker to his right, and the forward's driven shot rose high into the net.
Capello's low centre of gravity and movement was catching the eye, but Alli should have done better having been played in by him when he unsuccessfully tried to dribble round the keeper.
Halifax ended the half the far stronger side, with Alli, Cooke and Capello causing a lot of problems for the hosts: Alli was quick and direct, Cooke and Capello produced good movement and close control.
Town didn't get into the same flow or rhythm after the interval in what became a more scrappy game.
Both sides were lacking quality when trying to hurt the other, with too many passes going astray. Halifax's attacking sizzle had fizzled out.
Alli's low shot was saved by the keeper midway through the second-half after a turgid previous 20-odd minutes, moments before Doherty's effort bounced just the wrong side of the post with Tom Scott beaten.
Halifax ended the contest stronger, looking likelier to find a winner, but Turner nodded in a free-kick at the far post to hand the hard-working hosts victory.
Colne: Burton, Fagan, Steel, Winstanley, Mayor, Jones, Carney, Wallbank, Stowe, Weaver, Doherty.
Scorers: Weaver (7), Turner (88)
Shots on target: 3
Shots off target: 6
Halifax: Stott, Minihan, Debrah, Arthur, Triallist, Summerfield, Hunter, Cooke, Capello, Harker, Alli. Subs: Aliyu, Sinfield, Furtado, English.
Scorer: Harker (34)
Shots on target: 4
Shots off target: 13
Town man of the match: Milli Alli looked dangerous down Halifax's left, full of pace, had defenders backpedalling when he ran at them and could easily have scored.