The victory gave the Crusaders their second consecutive Lakes 8 Conference championship.
MCC finished its conference schedule with a 17-3 record.
Fruitport led 6-0 in the seventh inning, but MCC tied the game in the bottom of the frame to force extra innings.
The Crusaders scored the winning run in the bottom of the ninth with a two-out single by senior John Sanocki.
Sanocki and Duy Nguyen led MCC with two hits apiece. Robbie Bridges pitched two innings of relief to collect the win. Connor Schuitema led Fruitport with three hits while Parker Tawney added two.
Fruitport won the first game 6-4. Zach Miller pitched a complete-game victory for the Trojans, scattering six hits and striking out eight.
Fruitport was led by Jarod Wierengo with two hits. Mason Convertini had two hits for MCC.