Accomplice poachers told the victim's family that he had been killed by an elephant on Tuesday. Relatives notified the park ranger.
A search party struggled to find the body but eventually found a human skull and a pair of trousers on Thursday.
"Headless body found in topless bar"
The managing executive of the park extended his condolences to the family.
"Entering Kruger National Park illegally and on foot is not wise," he said. "It holds many dangers and this incident is evidence of that."
Kruger National Park has an ongoing problem with poaching and there remains a strong demand for rhino horn in Asian countries.
On Saturday, Hong Kong airport authorities seized the biggest haul of rhino horn in five years, valued at $2.1m (£1.6m).