Dozens of endangered were apparently killed by a swarm of bees in on Friday.
The 63 penguins were found dead on Friday at a colony in Simonstown, near Cape Town, according to a statement from South African National Parks (SANParks).
"The deaths occurred suddenly some time between Thursday afternoon and Friday morning," and experts started investigating the cause of death, the statement said.
"The post-mortems revealed that all the penguins had multiple bee stings, and many dead bees were found at the site where the birds had died," it added.
The preliminary investigation suggested the penguins died after being stung by Cape honey bees, SANParks said, but samples were still being tested to rule out other possible causes.
Alison Kock, a SANParks marine biologist, thanked the organization's partners, including the Southern African Foundation for the Conservation of Coastal Birds (SANCCOB) and the City of Cape Town, for their assistance in investigating the "unusual event."
"No more dead African penguins were found on site today, and we will continue to monitor the situation," Kock said in the statement.
On Sunday, veterinarian David Roberts from SANCCOB told the AFP news agency that bee stings had been found around the penguins' eyes.
"This is a very rare occurrence. We do not expect it to happen often, it's a fluke," Roberts told AFP.
African penguins are native to the coasts of South Africa and Namibia.
They are among the smaller penguin species, known for their irregular markings and loud voices.
The species is also in sharp decline, from a population of more than a million at the beginning of the 20th century to just 55,000 in 2010 -- when they were declared endangered.