Marius Els, 40, who was pictured balancing on the hippo's back, had been repeatedly warned that although friendly, Humphrey was still a wild animal and had to be treated as such.
The hippo was rescued as a calf during a flood of the Vaal River, which passes the land where Els farmed part-time.
Humphrey, estimated at around five-and-a-half years old, had been treated as a pet, and had learned to swim with humans.
The animal found a home with Els when it became too big for the people who had initially adopted it.
In August, the hippo was in the news when it was blamed for killing calves belonging to Els's business partner.
It also regularly broke out of its enclosure and chased golfers at the Orkney golf club.
At the time, Els said that the calf story had been intended to put him in a bad light after his business relationship with his partner soured, and that Humphrey's escapades on the golf course were to brighten up his social life.
Els said the sound of his voice would get Humphrey back home.
Netcare 911 spokesperson Jeff Wicks said that earlier this year paramedics had to rescue a 52-year-old man and his 7-year-old grandson who spent two hours in a tree after being chased by Humphrey while canoeing along the river that passes through the farm.
Els, who is survived by his pharmacist wife Louise, had called the 120kg hippo "loveable" and a "gentle giant".