Her rape and murder spurred women to march in the streets of major cities and rally behind an online campaign called #AmINext to call attention to the country's high rate of sexual violence.
A post on the royals' Instagram account called the death "a critical point in the future of women's rights in South Africa" and said the visit was "personally important" to Meghan.
Markle also spoke with Mrwetyana's mother, the post said, adding that "the Duke and Duchess had been following what had happened from afar and were both eager to learn more when they arrived in South Africa."
More than 100 rapes are reported every day in South Africa, and President Cyril Ramaphosa calls the country "one of the most unsafe places in the world to be a woman." He announced new emergency measures and vowed to be tougher on perpetrators, but some women weary of years of such pronouncements have suggested that South Africa bring back the death penalty for rapists.
The scope of the problem is well-known. More than 2,700 women -- and more than 1,000 children -- were murdered in South Africa last year, the government says. One in five women over age 18 have faced physical violence from a partner.
Women's empowerment is one of the many issues that Markle and Prince Harry are highlighting on their first official tour as a family with their baby, Archie.
She called attention to violence against women while in Nyganga on Monday.
"My husband and I have been closely following what you've been experiencing here -- as best we can from afar," she said. "But now that we are with you, we are eager to learn and see firsthand the work that you're doing, the vital work that you're doing, and that everything that is being done on the ground is making the great change that you not only need but that you deserve."
The 10-day, multi-country visit continued on Saturday for Harry with a meeting in Angola with the president of the southern African nation.
On Friday, Prince Harry followed in the footsteps of his late mother, Princess Diana, whose walk through an active minefield in Angola years ago helped to lead to a global ban on the deadly weapons.
The Associated Press contributed to this report.