Southern Boone took a 1-0 lead into halftime after converting a penalty kick after a handball called against Jefferson City.
Ethan Blake of the Jays tied the game with a goal with about eight minutes left in regulation. After a pair of scoreless overtime periods, the Eagles won the game in penalty kicks.
Southern Boone is now 6-0.
Jefferson City (5-1) is back in action Wednesday at Rolla.