The Black Cats were the aggressor in the first-half, and took a deserved lead in the 39th minute when defender Tyrese Dyce poked the ball into the net at the back post from a corner.
But The Magpies found a different gear in the second-half, with former Sunderland man Jay Turner-Cooke equalising after he deflected Joe White's effort beyond Jacob Carney.
Newcastle found the winner seven minutes later through Adam Wilson, who slammed the ball home at the near post to ensure The Toon left Wearside with all three points.
Story of the game
Sunderland boss Elliott Dickman made a number of changes to his side after their impressive victory over Leeds United under-23s last week. Tomorrow's first-team clash against Crewe Alexandra almost definitely impacted his selection – with the likes of Oliver Younger, Stephen Wearne and Will Harris all not named in the side.
Newcastle also made several changes to their team after their victory over Newcastle Benfield last week, with the surprise inclusion being former Sunderland man Jay Turner-Cooke, who made the switch over to The Magpies this summer.
There was never a chance of this Wear-Tyne derby being a slow-starter and just two minutes in, Sunderland should have had their noses in front.
Joe Ryder picked the ball up from deep, travelled 40-yards leaving the Newcastle defence behind and released himself through on goal, but he fluffed his lines and dragged his shot well wide of the goal.
Tempers flared just a few minutes after that big chance, Black Cats defender Tyrese Dyce picked up an early booking after a scuffle in the middle of the pitch.
If anything, that scuffle mellowed the game out, with the affair turning somewhat cagey an edge of your seat opening five minutes.
It took another 30 minutes for the next opportunity to come round – Sunderland pounced on Newcastle's attempts to play out of the back – a common trait throughout the first half – as the ball trickled wide to Kenton Richardson who teed up Harrison Sohna who blazed his shot from range well over-the-bar.
Sunderland's pressure in the late knockings of the half paid dividends, as they took a deserved lead in front of a home crowd.
Ellis Taylor's shot from range had to be tipped over for a corner – and from that corner, Dyce found himself in the perfect position at the back post to bundle the ball into the net.
Newcastle created next to nothing the entire half, but suddenly sprung to life when the ball fell to Lucas De Bolle a point-blank range but Jacob Carney was level to it and made a huge block to deny The Toon of an equaliser.
The final chance of the half came to the away side when Dylan Stephenson raced in on goal, but Carney did well again, getting low to make a routine stop.
Newcastle turn the game on its head and run out derby day winners
The second-half picked up where it left off, with Sunderland on top. A mix-up between defender and goalkeeper left The Black Cats with an open goal, but Sohna's audacious 45-yard effort sailed over the crossbar.
Despite Sunderland looking like they were going to double their lead, Newcastle drew level in this Wear-Tyne derby, but it came with a huge slice of luck as Joe White's curling effort deflected off Turner-Cooke that took the ball beyond Carney.
And just seven minutes later, The Magpies found themselves in front on enemy turf.
Some exquisite neat play from the away side saw Joe White play a killer pass to the left-hand side towards an unmarked Adam Wilson, who picked his head up and slammed the ball home at the near post.
Sunderland attempted to try and get themselves on level terms, but other than one notable attempt on target – that was palmed away to safety by Langley – it took them until the final five minutes of the game to look slightly threatening.
They found luck down the right-hand in particular in the final five minutes, and almost drew level if it was not for a goalmouth scramble being hooked away from danger.
Instead of looking for the corner, Newcastle looked to put the game beyond any doubt as White bursted through the Sunderland defence, but dragged his shot wide of the goal.
Sunderland – despite being spurred on by their home crowd – could not find their equaliser, meaning Newcastle left the Stadium of Light with a derby day victory.
With the win, The Magpies move into fourth place in the Premier League 2 Division Two table – with Sunderland remaining in 13th position.
Sunderland U23: Carney, Richardson, Dyce, Sohna, Almond, Xhemajli, Kachosa, Scott, Ryder, Taylor, Newall
Newcastle U23: Langley, Barrett, Bondswell, Young, Wiggett, Savage, Turner-Cooke, De Bolle, Stephenson, White, Wilson