The Turnbull Ground turned into a cauldron, with both teams and sets of fans battling for the bragging rights.
Though Boro didn't begin to boil over until the latter period of the second half, they still did enough to melt the dreams of Whitby.
Having felt enough cup pain of their own on Saturday, Boro boss Steve Kittrick decided to shake things up by making a number of changes.
Despite this, they soon found themselves under pressure as Whitby made a positive start.
The defensive frailties that have scarred recent performances soon reared their head as the dreaded set-piece once again began to haunt the visitors.
Keeper Tommy Taylor was at his best in the opening exchanges though, plucking the ball from the toe of striker John Campbell when he looked destined to score.
But as more and more balls were tossed into the box, Boro began to creak under the pressure.
That gauge was released a touch by the lively Michael Coulson, who was unlucky not to break his duck for the game when a Max Wright cross bobbled over his foot eight yards from goal.
Just a minute later it was Whitby who moved ahead.
There was a huge melee after a ball into the box and Niall McGoldrick reacted quickest when the chance presented itself from close range.
Taylor had to make another smart save straight from the kick-off. The stopper brilliantly tipping over a goalbound drive from the unmarked Kieran Weledji.
It was all about the Boro keeper in the moments that followed, as he got down well to save from Campbell.
Then Taylor spilled a corner into a packed penalty area, but then recovered to deflect the ball over the bar.
The returning Danny Stimpson was thrown on at the break in place of Matty Turnbull as the Boro bench searched for defensive solidity.
This glue seemed to set, though Boro were aided by a flat start to the new half and a lack of home ambition.
Former Blue Billy Logan was then thrown into the fray on the hour and his introduction also had consequences.
Logan soon ploughed his way through the right-side of the Whitby defence and swung a ball into the centre. Charlie Binns, playing his first minutes in some time, stooped and powered a header past Shane Bland.
Boro then threw their final substitute on in the shape of Nathan Valentine, another switch that would eventually pay off.
With Whitby rocking on the ropes, Boro looked to land that telling blow.
A number of sighters followed, with Coulson and Dave Merris going so close to driving a wedge between the sides.
Then the game finally broke into a derby contest in the final 10 minutes, as play swung from one end to another.
Whitby could have moved ahead when Steven Snaith stole away at the back post, but his header was superbly saved by Taylor.
Then Bland got lucky when Coulson lobbed the ball straight into his arms when the striker broke free of the Whitby back-line.
The all-important goal came with just a handful of minutes left, as Nathan Valentine was picked out in the box. The midfielder didn't get the best contact on the ball, but he did enough to send it rolling into the bottom corner of the net.
Boro had to don the tin hats for the final moments, but Whitby failed to forge an opportunity and Boro booked the cup success.