Scott Van Zyl was killed last week on the banks of the Limpopo river, said Sakkie Louwrens, director of a South-African crime-fighting NGO.
He said Mr Van Zyl disappeared during a hunting safari last week.
His death is the latest in a series of fatal crocodile attacks in Zimbabwe.
Mr Louwrens told the BBC that Mr Van Zyl had gone on a hunting trip on the Zimbabwe-South Africa border with a local tracker and a pack of dogs.
He said the pair left their vehicle and went in different directions in search of crocodiles.
A search and rescue operation was launched after Mr Van Zyl's dogs returned to their camp without him.
The hunter's footprints were traced to river bank alongside his discarded rucksack. He was married, had two children and took foreign clients on hunting trips.
Mr Louwrens said staff from the Heritage Protection Group - an organisation which he heads and helps police fight crime in South Africa - informally helped the Zimbabwean authorities conduct the search.
"Permission was given for three Nile crocodiles in the area to be shot, and one of them contained Mr Van Zyl's remains," he said. "Subsequent DNA tests have proved the remains to be those of Mr Van Zyl."
At least four fatal attacks by crocodiles have been reported in Zimbabwe this year.
One conservation group meanwhile has condemned the circumstances of his "senseless" death.
"[He] shouldn't have been hunting in the first place. Animals in the wildâ€¦ are wild! They are living, thinking beings with instincts for survival," a statement by One Green Planet said.
DNA tests on the carcass of a crocodile shot in Zimbabwe have confirmed that it contains the remains of a missing South African hunter, an investigator has told the BBC.