Mugabe, who is being sought by police after allegedly attacking a 20-year-old model at a Johannesburg hotel last weekend, flew home with her husband on Sunday.
But he appeared to have cut short his visit, skipping the second day of talks among leaders of the Southern African Development Community (SADC).
South African police had said they were on high alert to make sure that Mugabe's 52-year-old wife did not leave the country with officials reportedly weighing up whether to issue an arrest warrant.
The first lady is alleged to have assaulted Gabriella Engels with an electrical extension cable on August 13 at the hotel where the model was staying with Mugabe's two sons who have a reputation for partying.
Engels said she suffered deep cuts to her forehead and the back of her head and has opened a police case alleging assault with intent to do grievous bodily harm.