Everton beat Ben Dawson’s side 1-0 at Goodison Park to lift the trophy.
United goalkeeper Nathan Harker made a string of saves before the break, and and Morgan Feeney’s 59th-minute header would prove to be the difference between the two sides.
Elias Sorensen, nominated for the Premier League 2 player of the season award after scoring 20 goals, came off the bench before Feeney broke the deadlock.
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Newcastle will now start preparations for their promotion play-off game against Southampton.
Dawson, United's coach told nufc.co.uk: "I couldn't be prouder of the lads for the season they've had so far. Tonight was disappointing, but I didn't think there was a lot in the game.
"I thought we controlled the ball really well, and they controlled around their goal really well. Neither team really looked like scoring in open play, so it was always going to come down to a set play or individual error, which proved to be the case.
"It was a cheap free-kick to concede from which allowed them to get their noses in front. The rules then changed and we were chasing the game a bit.
"We made a few changes, and it looked like we controlled the ball, but we didn't seem to have enough in that final third to open up and create a good opportunity to score."
Meanwhile, manager Rafa Benitez has called up Victor Fernandez for a first-team training session.
The winger had hip surgery late last year after an injury-hit start to the season.
Fernandez tweeted in November: “This start of the season has been complicated, with some problems that have finally made me go through surgery.
"I have had an operation in the hip, but luckily everything went very well, and I am already thinking on recovering as soon as possible to play again.”
Fernandez has since recovered from the operation.
And the 21-year-old took part in yesterdeay’s first-team training session at Newcastle’s Benton HQ ahead of Sunday’s season-ending Premier League fixture against Fulham at Craven Cottage.
NEWCASTLE UNITED: Harker, Sterry, Gibson, Bailey, Cass, Watts, Allan (Longelo, 81), Sangare (Toure, 73), Charman (Sorensen, 55), M Longstaff, Roberts.