Gerald Samson scored a first half brace before Matutu captain Tony Oloo converted the consolation goal from the spot kick.
Speaking after the win, Koderobara football coach Moses Otieno praised his charges for being mentally strong despite the prolonged stoppages.
"Congratulations to the boys. These hardworking students deserve the win especially if you look at the run we have had. It is our first time to get to the nationals and we will be ready," said Otieno.
Koderobara finished runners up in Group A where they faced defending champions Agoro Sare, Kisumu Day and Ong'icha.
The Migori County champions will now represent Nyanza Region in the finals set to begin on July 29.