Ebwali in the process dethroned defending champions St Anthony's Boys Kitale, who were knocked out in the regionals by Kabarnet.
It is also an improvement from their third place finish in 2019, their last appearance at the nationals.
"I have been fighting to get this title since 2014 without success, but finally I have managed. This win is one of a kind because we have beaten a strong team," said Ebwali head coach Francis Muhambe.
In the girls' category, Rift Valley champions Wiyeta Girls, who are known for producing top players including Vihiga Queens and Harambee Starlets' Jentrix Shikangwa, reclaimed the title they lost five years ago after edging out Dagoretti Mixed Secondary on post-match penalties
Wiyeta claimed their 10th title and first since 2018 after they saw off Dagoretti Mixed Secondary School 4-1 on post-match penalties after the match ended in a 0-0 draw in regular time.
Wiyeta goalkeeper Velma Auma emerged the darling of her team and fans after she saved two penalties from Patience Kasiutawa and Miriam Susan to give her side the memorable win.
Dorine Aujat, Praxidis Shirikwa, Lavenda Waswa and Sharlyne Opisa were on the spot for Wiyeta.
"I am very happy we are taking home the 10th title," said Wiyeta coach Edgar Manyara.
Wiyeta dethroned defending champions Nyakach Girls who failed to reach the nationals after losing to Kobala Mixed in the Nyanza Regional games.
Wiyeta Girls, Ebwali Secondary, Highway Secondary and Dagoretti Mixed will all represent Kenya at the East Africa games.