Edgehill had the ideal start as forward Luke Jones beat the offside trap and evaded the attentions of the Pier defence to slip the ball past keeper Scott Wardman and then ran around him to tap the ball into an empty net.
The league leaders doubled their lead soon afterwards, with Jones again nipping through and sliding his shot past Wardman, left-back Niall Gibb having miscontrolled when through on goal for Pier a few seconds earlier.
Wardman then made an amazing save to deny Jones and Gibb an outstanding block to keep Pier in the game.
This proved vital as Gibb then made an excellent run down the left flank and after a quick one-two rifled his shot low past Edgehill keeper Chris Ferrey.
Wardman made yet another top stop to deny Jones but Edgehill were soon two goals in front again when skipper Joe Gallagher turned neatly and smashed a stunning shot into the top corner.
Both sides were reduced to 10 men just before half-time when the teams got involved in a scuffle after Sean Exley went to ground in the area, Neil Thomas showed a straight red for Pier and Kieran Link a second yellow for their part in the melee.
Exley was also shown a yellow card after the dust settled.
Pier had a strong appeal for a penalty rejected on the stroke of half-time, Will Jenkinson receiving a caution for his protests after the half-time whistle.
Edgehill seemed to adapt better to the spaces left by the 10-a-side contest, and went 4-1 up through a deflected shot by skipper Gallagher, and this soon became 5-1 after a low shot from defender Lloyd Henderson.
Pier grabbed a second late on when Jamie Bradshaw's 30-yard low drive crept through the grasp of keeper Chris Ferrey, but Edgehill had already done more than enough to win the cup.