The championship is the first in school history for the Lions (8-2), who will play Southwestern in a state regional final Saturday back at Sahlen's Stadium.
Tournament MVP Mike Berardo ran for 177 yards and two touchdowns for Wellsville, who led 20-8 in the second half.
Kyle Busch scored from ten yards out and Evan Englert added a two point run, cutting the lead to four.
Glen Rifenburg answered with a 36 yard field goal for Wellsville that turned out to be the difference in the game.
Englert hit Dean Bembower on a dramatic 40 yard TD pass with 14 seconds left. Wayland-Cohocton did not try to kick on any of their touchdowns, so the Eagles went for two and the win. Busch rushed left, but Wellsville swarmed and stopped Englert at the four yard line.