During the discussions Markle, aged 38, told the academics and students: "When a woman is empowered it changes absolutely everything in the community."
She announced three new gender grants for the University of Johannesburg, Stellenbosch University and the University of Western Cape Province from the Commonwealth organisation.
"The goal here is to be able to have gender equality, to be able to support women as they are working in research and higher education roles," she said.
She added: "And also to be able to have workshops, convene things that are really helping people understand the importance of gender equality.”
The duchess and her family are on a royal tour of Africa which kicked off in Cape Town last week, with husband Prince Harry and son Archie.
Harry is currently on a mission to Malawi, where he also paid tribute to a fallen British soldier recently killed by poachers in a game reserve while on a training mission of that country’s game rangers.
Markle met the academics and students during a roundtable discussion with one of her patronages, the Association of Commonwealth Universities -- assigned to her and Prince Harry to look after by Britain’s Queen Elizabeth, who is the head of the Commonwealth.
However, the royal trio will be reunited on Tuesday as Prince Harry flies back to South Africa from Malawi where he ends his visit with a tour of a health centre.