Having trailed the Magpies from early on, Boro had fought back to take a 2-1 lead, but their north east rivals refused to die as they inflicted two late knockout blows at the Riverside to progress with a 3-2 success.
Middlesbrough 2-3 Newcastle United
The FA Youth Cup Fourth Round Proper
Thursday 8 January
Riverside Stadium
The visitors took the initiative after 10 minutes when a deep cross from the right was played back across goal by Callum Williams, and James Cobain was on hand to turn home at close range.
But the hosts drew level on the half hour mark, with England U18s midfielder Callum Cooke crossing from the left for Alex Pattison to head home an equaliser, and it remained even until the clock reached 66 minutes as the former proved to be a thorn in the Newcastle defence once more.
The 17-year-old edged Boro in front when he was brought down inside the area, and Cooke dusted himself off to send his Young Lions team-mate Freddie Woodman the wrong way from the spot. The pair were on the same side when England U17s won the European Championships last summer, Cooke scoring one of the penalties in a successful shoot-out victory that secured the prize.
Now in the ascendency, the home side were unable to add to their advantage and they were pegged back on 85 minutes – Daniel Barlaser stroking home to level the scores from 12 yards.
Both sides had chances to notch as the game neared its end, but it was Boro who had the best opportunity to seal it seconds before the 90 were up. Cooke sent Junior Mondal clear just left of centre, but he dragged a low shot wide – and it was to prove costly.
Sweeping forward deep in additional time, Newcastle worked their way into the Middlesbrough penalty area, forcing a save from Tom Dawson, but they did not waste the rebound as Sean Longstaff slotted home the winner.