Mayo, son of former Bafana Bafana striker Patrick, could not help his side to victory in the final as they lost 3-1 to English giants Arsenal at Umlazi's King Zwelithini stadium as The Gunners retained the title they won last year.
Khanyisa also won the Golden Boot by finishing with six goals in four matches, one ahead of Arsenal's Stephy Mavididi.
READ ALSO: Notoane hails his runners-up
"Being a top goalscorer, I wanted to step-up in this tournament to show that I can score goals for the country and myself, which I did," he said after the final.
"I'm so proud of myself that I got the Player of the Tournament. It means a lot to me; it's an achievement that shows I can up my game.
"Having said, I feel today was not our day. We planned it out that we were here to win the trophy. Unfortunately we didn't play to our strengths and Arsenal outclassed us.
"Now we are runners-up of the tournament, but I'm proud of the guys and as South Africans we are proud also."
Mayo, who was part of the South African team at the FIFA Under-17 World Cup last year in Chile, may be drafted into the SuperSport United senior team ahead of this coming after Phumelele Bhengu decided has parted ways with the club.
READ ALSO: Bhengu parts ways with SuperSport
The 17-year-old, who will eligible for Durban Under-19 tournament again next year, will form part of South Africa Under-20 later this year at the COSAFA Under-20 Championships in North West province in December, and also the African Youth Championships in Zambia next March.