Scarborough's Matt Bancroft was the hero, saving 2 of 10 penalties he faced in the shoot out.
The game, at the T6 Academy in the heart of Middlesbrough, started in electric pace with the under 23's of Middlesbourgh dominating the opening exchanges and scoring an early goal. Howells tapping in from a low cross on the 3G surface.
But from then, Scarborough were in charge and remained so throughout the game.
The Seadogs created plenty of chances with Harry Green the standout player weaving his magic down the left hand side.
On loan Finlay Barnes saw a shot hit the woodwork for Scarborough but the visitors were rewarded in the 2nd half when sub Lewis Maloney delivered a corner, with Harry Green nodding it in past Middlesbrough keeper Fisher.
Scarborough had chances to win it in normal time but the game went straight to penalties after 90 minutes.
Frank Mulhern missed Scarborough's first and with Middlesbrough scoring their first 3 it looked like it might prove costly.
But Bancroft made a truly spectacular save from a Middlesbrough penalty which looked destined for the top corner to level things up before the shoot out went into sudden death.
Scarborough scored every one of their penalties, aside from the initial Mulhern miss, and Bancroft made another save for Middlesbrough's 10th penalty, ending the game and seeing Scarborough progress to the next round.
Here's the moment Boro beat Middlesbrough U23's in the penalty shoot out:
Boro boss Jono Greening said he was pleased with the performance:
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