United's second-string, which included Magpies midfielder Isaac Hayden in their starting line-up, fell behind in the first-half at The Shay following Andrew Olubawori's fortunate finish after blocking Charlie McArthur's intended pass.
Johnny Emerson, however, levelled the Group C encounter towards the hour mark before Ben Parkinson's close-range rebound, his third goal in his last four away matches at under-21 level, fired the visitors ahead before an ill-tempered conclusion saw Halifax reduced to ten men following Festus Arthur's red card.
Ahead of their first game in the inaugural competition, Diarmuid O'Carroll made three changes from the side which claimed a 2-0 win against Blackburn Rovers Under-21s in the Premier League 2 on Friday as Hayden, who has recorded 118 English top-flight outings for the Magpies, was handed a start along with Irish centre-back Cathal Heffernan and Emerson.
The young Magpies began the cup contest in positive fashion as Jay Turner-Cooke, who netted a brace in United's 2-0 league win against Blackburn last week, went close to netting in successive matches, latching onto Alfie Harrison's accurate cross into the penalty area but saw his low effort was parried by Halifax goalkeeper Nathaniel Ford.
In the 17th minute, Newcastle fell behind in unfortunate circumstances as McArthur's pass from the edge of his own box was blocked by Oluwabori before the ball landed in the left-hand corner of the net.
United goalkeeper Aidan Harris, who was named on the bench for the Magpies' UEFA Champions League Group F draw away at AC Milan in September 2023, produced a key stop to prevent Aaron Cosgrove doubling the hosts' lead as the 17-year-old, who joined Newcastle's youth set-up in 2017, tipped the striker's curling shot from the edge of the box around the left-hand post.
In the second-half, Harris denied Halifax skipper Jamie Cooke from extending Town's advantage, beating away the Halifax captain's ferocious drive before the Houghton le Spring-born shot-stopper held Tom Pugh's powerful drive minutes later.
In the 59th minute, Newcastle levelled the clash through Emerson as the Carlisle-born winger raced onto Turner-Cooke's pass inside the box before emphatically lifting the ball into the net.
Trevan Sanusi, introduced from the bench after United's equaliser, went close to firing Newcastle ahead as the Birmingham-born winger, a representative of England at under-18 level, raced onto Emerson's pass but, after dangerously cutting inside from the left flank, saw his deflected effort fly narrowly wide of the left-hand post.
Harris was on hand to deny Cooke from regaining Halifax's one-goal cushion, pushing out the striker's drilled effort towards the front post out for a corner.
In the 70th minute, Newcastle took the lead through Parkinson. After the Durham-born forward's initial header from Leo Shahar's teasing corner struck the crossbar, the 19-year-old was on hand to turn the loose ball into the net.
Halifax were reduced to ten men in the final stages as Arthur picked up a second yellow card after an ill-tempered affair embroiled between both sides after Turner-Cooke was left on the receiving end of a late foul, with the hosts appealing for a penalty seconds prior.
Despite five minutes of stoppage-time, Newcastle held firm to record maximum points, getting their National League Cup campaign off to a winning start.
Newcastle United Under-21s: Aidan Harris, Leo Shahar, Cathal Heffernan (c), Charlie McArthur, Dylan Charlton, Isaac Hayden (Anthony Munda 60), Travis Hernes (James Huntley 70), Jay Turner-Cooke, Alfie Harrison (Trevan Sanusi 60), Johnny Emerson (Josh Donaldson 70), Ben Parkinson (Ellis Stanton 80).
Subs not used: Ciaran Thompson, Adrian Janusz.
