Meghan stayed on in Cape Town where she visited charity Mothers2Mothers, and undertook a surprise visit to pay her respects to Uyinene Mrwetyana, a 19-year-old student who was raped and killed at a post office in Cape Town in late August.
The royals will be reunited in Johannesburg on Tuesday, and the Duchess and Archie were seen boarding a plane for the city on Sunday.
In the cute photos, Meghan is cuddling Archie as they walked onto an aeroplane together.
Prince Harry followed in his own mother's footsteps during a visit to a de-mining site in Dirico, Angola, to raise awareness of the danger and prevalence of landmines that still exist today.
In 1997 Diana, Princess of Wales visited Huambo to bring global attention to the crisis of landmines and the people whose lives were being destroyed.
WATCH: Meghan Markle responds to becoming Queen!