After a goalless first-half at the King George V Ground, Whitby fell behind with a quarter-of-an-hour to play following Mustapha Abdullahi's tap-in before Alfie Doherty levelled the clash in the closing stages, netting against his hometown club in the process.
Summer signing Jake Charles then continued his eye-catching pre-season form to secure the comeback victory two minutes later to ensure that the Seasiders retained the Mickey Skinner crown.
Nathan Haslam handed was without both Shane Bland and Nick Cranston, meaning that a Trialist was given the chance to impress between the posts, while 15-year-old Connor Marsay was named on the substitutes' bench. He would later make his first appearance for the First Team as a second-half substitute.
After a slow start to proceedings, Aaron Haswell went for goal with an effort from distance in the 16th minute. He was denied by Robert Dean, who parried Haswell's effort before Jake Charles was unable to keep the ball in play and keep the move alive.
Guisborough find their first real opening of the match four minutes later as Abdullahi advanced forwards before twisting and turning on the edge of the area. An eventual shot did come in but Whitby defended the situation well between Gary Liddle and Frankie Whelan at centre-half.
In the 30th minute, Priestley Griffiths picked the ball up around 30 yards out and took a couple of steps forward before striking for goal but he could only fire wide of Robert Dean's right-hand post.
Kyle Davies went close for Guisborough shortly after, forcing Whitby's Trialist 'keeper into a strong save with his left hand following a header before Whelan came to Whitby's rescue, getting back well to keep Guisborough out following former Whitby man Bradley Mills' cut-back.
Griffiths was next to go for goal for the Seasiders with a dipping free-kick, but Dean wasn't troubled, while Connor Smith did all he could to help the Blues gain the initiative before the break when he floated a cross in towards the back post. Aaron Haswell knocked the ball down before James Frazer cleared behind for a corner which came to nothing ahead of the half-time rest.
The Seasiders missed a great opportunity to break the deadlock after eleven minutes of the second half as Jassem Sukar saw his header tipped away by Dean following a corner.
Half-time substitute Soni Fergus was perhaps fortunate to only see yellow as he went into the book following a strong challenge in midfield just past the hour mark.
The 66th minute saw Lewis Hawkins go for the spectacular but his effort was never realistically going to trouble Dean in the host's goal.
Just a minute later, another substitute, Nathan Thomas, cut in from the right and hit the target. Once again, Dean was equal to the strike however.
In the 74th minute Guisborough took the lead as a long ball forwards caught the Trialist shot-stopper in no man's land on the edge of his area, allowing the ball to float over his head and present Abdullahi with an open goal to give his side the lead.
But just as it seemed the game would come to a disappointing conclusion for Haslam's men, Doherty stepped up after receiving the ball on the left before cutting inside and firing a rasping effort beyond Dean.
And despite struggling to create clear-cut opportunities all night, Whitby were soon ahead after Thomas was left in acres of space on the right before playing a low ball across the face of goal for Charles to fire home emphatically just two minutes later.