Shaffer's homer made it 3-0 after one inning.
Jersey Shore started the three-run third with four straight hits to move in front, 4-3.
Tylor Moyer tripled in one run and scored the other on a J.T. Fogleman single to put Milton back ahead, 5-4, in the fourth.
Milton stayed in front until Jersey Shore forced an 11-11 tie with five runs in the bottom of the eighth.
Both teams scored once in the ninth to set up extra innings.
Shaffer and Mark Artley each had three of Milton's 15 hits. Michael Jacobs -- who drew three walks and scored three times -- and Tylor Moyer added two each.
Shaffer scored three runs and drove in three.