Magaia's two goals came in the space of eight minutes as she tapped home from close range in the 63rd minute and added a second in the 71st from a similar position.
A lapse of concentration saw South Africa give away possession to allow Morocco to pull a goal back in the 80th minute through their English-born striker Rosella Ayane (26).
It set up a nervy finish, which included nine minutes of added time, in front of a capacity crowd in the Moroccan capital Rabat.
It was South Africa’s first title after having finished runners-up five times, including the last edition in 2018.
Morocco were playing in their first final and will be heading with South Africa to next year’s Women’s World Cup along with the two beaten semi-finalists Nigeria and Zambia.
The Cup of Nations serves as Africa’s qualification event for the tournament in Australia and New Zealand.
