Former Jersey 1st team flyer Gareth Jefferies put the home side ahead in the first half, but Guernsey's Paul Smith equalised before the break, with the visitors going in front with a Dave McGall score.
Crucially, when Jersey crossed the line through Alex Walker, that try was converted by Will Church.
Those two points were the margin of victory at the end, although Guernsey will be rue two kickable penalty chances being spurned near the end.
Danny Curzons picked up the trophy for the Jersey side.