Kenyan champions Wiyeta fell 2-1 to Uganda's St Noa Girls Secondary School, while debutantes Highway lost 2-0 to another Ugandan outfit, Kibuli Secondary School.
Highway, who had knocked out record 13 times champions St Mary's Kitende 1-0 in Thursday's semifinals, were undone in the final by a goal on either half from Kibuli's Dominic Ayella.
The winger struck a sweetly taken free kick on the stroke of halftime, before poked home a rebound after Highway keeper Paul Okumu parried a rebound from a powerful shot on his path in the second half.
Highway captain Teddy Ochieng said Kibuli were deserved winners.
"I'm disappointed we lost because we worked so hard to reach the final. They capitalised on our defensive mistakes and punished us. We have gained experience and I am confident we will come back stronger next year," Ochieng said.
It is Kibuli's first title after twice losing in the final in 2011 and 2014. Highway had beaten Kibuli 1-0 in the preliminary stages of the competition.
A late goal from Wiyeta forward Shalyne Opisa was not enough to help the Kenyans, who were bidding, to reclaim the title they won on 2017.
St Noa had took a 2-0 lead thanks to Sylvia Kabene and Erica Kanyamuneze and held on despite Wiyeta's push in the injury time.
"We did not utilise our chances and at this stage and it was very costly," Wiyeta coach Edgar Manyara said.
At the International School of Moshi (ISM), Kenyan boys' basketball champions Dr Aggrey High School were outwitted by defending champions Buddo Secondary School, losing 62-39.
Uganda also retained the girls' basketball title after St Mary's Kitende dethroned holders St Noa 72-69.