Scarborough started brightly, passing the ball around well and dominating possession.
They were soon rewarded when a well-taken Liam Love free-kick was headed on by Nathan Dolphin to the back post for Freddie Lockey to tuck into the corner to make it 1-0.
Boro continued to dominate and Oliver Hesketh picked up the ball in the middle of the park, rode a couple of challenges before playing the ball through to Dolphin, who fired it past the keeper to make it 2-0.
Hesketh was involved again minutes later when he raced into the box with the ball only to be taken down by a Shiptonthorpe defender, leaving the referee no choice but to point to the spot.
Riki-Lee Green stepped up to take the spot-kick only to see it finely saved by the keeper, but Green was first to the rebound to slot home Scarborough’s third.
Just before the break Shiptonthorpe pulled one back with a superb lob that left Regan Exley in the Scarborough goal with no chance.
Shiptonthorpe made life difficult for Scarborough early in the second half and pulled another goal back with a finely-taken free-kick.
With only minutes left on the clock Shiptonthorpe broke free and Scarborough’s keeper Exley was faced with a one-on-one to keep Boro in the lead and he pulled off a great stop to see Scarborough win 3-2 and go through to the Plate final.
Delighted manager Paul Exley said: “It’s easy to forget that 12 of these players are Under-12s playing up a year in the Under-13s league and the team only got together six months ago.
“They impress me week in-week out with their determination and this is nothing less than they deserve.”