Kekana broke the deadlock in the 70th minute with a right-footed effort from outside the box that was confirmed by a VAR check.
South Africa withstood waves of pressure as Morocco threw everything in attack in search of an equaliser in the remaining 20 minutes plus added time.
The North Africans came close on several occasions but could not find an equaliser thanks to some desperate defending.
South Africa lifted their first-ever youth continental tournament and became the 12th different nation to be crowned champions.
