The young Magpies fell behind in the opening stages of their final Northern Group F encounter following Ellis Taylor's strike at a rain-sodden Exercise Stadium before Alfie Harrison drew the visitors level on the stroke of half-time, firing the ball home from Harrison Ashby's pass.
Tom Curson's commendable effort after the hour mark regained the hosts' one-goal cushion before the Town substitute struck again in the closing stages to round off Newcastle's involvement in this season's competition.
Adam Lawrence made four changes from Saturday's 3-2 win against Burnley in the Premier League 2 as 16-year-old midfielder Sam Alabi, who has captained England at under-17 level, was handed his full debut for United's second-string while Seung-soo Park, Charlie McArthur and James Taylor all returned to the starting 11.
After observing two minutes of silence on Remembrance Day, Magpies skipper Cathal Heffernan produced a heroic block to prevent Reece Smith's goalbound shot before the loose ball fell into Taylor's path inside the box, who fired the ball narrowly wide of the right-hand post.
In front of 1,469 spectators, including 146 travelling away fans, Newcastle trailed in the 12th minute through Taylor as the Hartlepool-born midfielder was granted space to advance into the box from the right flank before placing the ball into the roof of the net.
United's youngsters were fortunate not to fall further behind after the half-hour mark as Smith dangerously cut inside from the left flank before drilling a ferocious attempt wide of the far post.
With the half-time whistle nearing, Newcastle found themselves level in the fourth of six additional minutes through Harrison's leveller. After Neave was fouled after passing the ball into Ashby's path, referee Richard Aspinall allowed play to continue before the Magpies right-back teed up Harrison, who placed a powerful first-time effort beyond Town goalkeeper James Belshaw.
Sean Neave was unable to net his tenth goal of the season at under-21 level after the restart as Ashby's teasing cross from the right wing found the Winlaton-born forward inside the penalty area but his stretching volley was directed wide of the target.
United's youngsters remained on level terms shortly after despite Taylor hitting the post for the hosts as the Harrogate midfielder's cross-cum shot from the byline deflected onto the foot of the front post.
Newcastle goalkeeper James Taylor produced a key stop to deny his namesake from doubling his and Harrogate's goalscoring tally, pushing away a fizzing effort from the edge of the box before Shawn McCoulsky's rebound from tight angle flew across the six-yard area.
In the 64th minute, Newcastle conceded for a second time as Cursons netted for Harrogate, collecting Levi Sutton's pass before his curling effort from the edge of the box flew into the far corner via the left-hand post.
Newcastle's hopes of equalising for a second time took a difficult blow as Cursons netted his second goal of the evening. After Taylor's initial shot from the edge of the penalty area was parried by Taylor, the Harrogate striker was on hand to steer the rebound into the net.
Newcastle United Under-21s: James Taylor, Harrison Ashby (Ciaran Thompson 62), Cathal Heffernan (c), Ben Parkinson (Joe Brayson 62), Charlie McArthur, Alfie Harrison (Thomas Bryant 83), Anthony Munda (Scott Bailey 46), Sean Neave (Darren Palmer 88), Seung-soo Park, Miodrag Pivaš, Sam Alabi.
Subs not used: Adam Harrison, Dylan Charlton.
Photograph courtesy of Harrogate Town Association Football Club
