With chances at a premium throughout the 90 minutes, both sides produced disciplined defensive displays, leaving the trophy to be decided from the penalty spot. Whitby ultimately held their nerve, with goalkeeper Jack Norton proving the hero by saving Guisborough's fourth penalty before Sam Kay converted the decisive kick.
The hosts made an encouraging start and nearly opened the scoring inside three minutes. Stan Hewitt tried his luck from distance with a right-footed effort that flashed narrowly wide of the target, providing an early indication of Whitby's attacking intent.
Guisborough responded in the seventh minute when Matthew Wilshaw broke through after the offside flag stayed down. However, Norton reacted well to make a strong save at his near post and keep the scores level.
Whitby continued to enjoy promising moments in the opening half. Callum Hickman was involved on several occasions, first chipping a left-footed effort into the hands of Ryan Catterick after 11 minutes. Two minutes later, impressive work down the flank from a Whitby trialist created another opportunity, with Hickman again testing Catterick, only for the Guisborough goalkeeper to gather comfortably.
The Seasiders thought they had broken the deadlock after 14 minutes when Stuart Rose found the back of the net, but celebrations were cut short as the assistant referee's flag was raised for offside.
As the first half progressed, both defences settled into the contest and clear-cut opportunities became increasingly rare. Rose came closest for Whitby before the interval when a loose ball dropped kindly for him on the edge of the area, but his strike was directed straight at Catterick.
The second half followed a similar pattern, with both teams organised and difficult to break down. Guisborough created one of their better opportunities in the 63rd minute when Wilshaw drove a low effort towards goal, but Norton was equal to it and made a comfortable save.
Whitby responded almost immediately through Tolou Oseyemi. After embarking on a direct run down the left wing, the attacker cut inside and unleashed a powerful effort that drifted wide of the far post.
Despite both sides continuing to search for a breakthrough, neither goalkeeper was seriously troubled during the closing stages. The contest therefore moved to penalties, where composure from the spot would determine the destination of the trophy.
Guisborough converted through Joe Ferguson, Leo Robinson, Harvey Coates and Josh MacDonald, but Norton's save from Jack Bailey's fourth penalty proved decisive. Whitby were flawless with their five spot-kicks, as Lucas Reid, Charlie Stirland, Stan Hewitt and Marley Grant all found the net before Kay stepped forward to calmly dispatch the winning penalty.
The successful shootout secured the Mickey Skinner Memorial Trophy for Whitby Town, rounding off a hard-fought encounter in which defensive resilience and goalkeeping quality were ultimately the defining factors.