Ben Parkinson, who made his Premier League debut for his boyhood club during last season's away clash against AFC Bournemouth in November 2023, opened the scoring at the Lamex Stadium against a Spurs side who lifted the Premier League 2 title last term.
The visitors then held firm to record an impressive victory and clean sheet in Hertfordshire, moving into sixth place of the division in the process.
Three changes were made from the side which claimed a 1-1 draw against Sunderland on Monday as 17-year-old goalkeeper Aidan Harris, who signed his first professional contract with United last month, and defensive full-backs Leo Shahar and Dylan Charlton were all handed starts in Stevenage.
In the 15th minute, Newcastle took the lead as Parkinson netted his first goal of the 2024/25 season as the Durham-born teenager racing onto Jamie Miley's pass before firing the ball past Spurs goalkeeper Josh Keeley.
Parkinson and Trevan Sanusi, who made his Magpies first-team debut in a pre-season friendly win against Hull City last month, were unable to extend Newcastle's lead further in the second-half but their misses would not prove costly as United's second-string recorded a positive win against the North London outfit, who had suffered a mere two league defeats last season.
Newcastle United Under-21s are back in action on Friday, 30th August when facing an away clash against Derby County at Causeway Lane, home of non-league outfit Matlock Town (kick-off 7pm BST).