The result sparked unprecedented scenes of celebration from the boys and supporters who had travelled the road to Auckland for the weekend.
The girls' team also claimed a bronze medal.
Kayes said he knew his young side had the necessary talent.
"I knew the boys could do it, they stood up, believed in themselves and each other and went out and smashed it," he said.
"Their defence today has been outstanding and that's what set the platform for them creating the goal opportunities. I'm hugely proud of what they have achieved."
Under-16 girls' coach Paul Kayes was impressed the girls dug deep to come from behind in beating Waitakere City 6-5 for their bronze medal.
In addition, Richard Sneddon was named the boys' MVP, while Patrick Low, Cayne Dew and Malia Josephson were all named in tournament teams.