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Muhammad Ajsal and Naseeb Rahman scored in a convincing 2-0 win for Kerala.
Seven-time champions Kerala edged Goa 4-3 in their opener.
Goalkeeper Hajmal S was announced as vice-captain of Team Kerala on Friday.
More than 150 cases were recorded in just two days in an injury-book on the senior boys' football event as part of Kerala School Games in Kochi.
Calicut bounced back from a goal down to win 2-1 in the first semifinal.
In Malappuram win, Kombans would go out on goal difference because both sides will be level on every other aspect.
Calicut goalkeeper Vishal Joon was sent off in the 87th minute.
The Thiruvananthapuram side scored twice in the second half to beat the Kannur side 2-1.
The Kombans scored a penalty and saved one in a 2-0 win.
The visitors won 4-1 with two goals each scored in either half of the contest in Thiruvananthapuram.
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