"One of them has already rebeached in Simonstown," said National Sea Rescue Institute spokesperson Craig Lambinon on Sunday.
"It is still alive and we are trying to save that one but its health has also deteriorated quite substantially."
The five had been placed on trailers at Noordhoek Beach and transported to the Simonstown naval base, before being taken out to sea.
Lambinon said nine other whales had been humanely euthanansed, while another five had died naturally.
The 19, mostly adult, whales beached on Sunday morning. Police, sea rescue and other services helped keep the mammals alive by using sheets and water.
The beach was closed and residents were urged to stay away. Attempts to refloat them had failed.
Reason whales beach
Marine biologists have said they do not fully understand why whales beach but there are many theories.
KwaZulu-Natal Sharks Board head of operations Mike Anderson-Reade said one theory was that when a leader of the pod gets caught in shallow water, so did the others.
"And then they get disorientated and find their way to shore," he said.
Another theory was that when a lead whale gets ill, it beaches and the others follow.
"But these are all just theories, the reason is still unknown."
Scientific American on its website said some environmental activists had suggested that mass strandings of dolphins, whales and other marine mammals were as a result of human impacts of pollution, shipping noise and, in some cases, military sonar.
The beaching of the pilot whales was possibly the first-ever mass stranding of these creatures on the South African coast.
"I don't think we've had a mass stranding of pilot whales before," said a marine life expert, who declined to be named for professional reasons.
Pilot whales are a type of toothed whale and there are two species – short finned and long finned.
"It's possible these are long-finned pilot whales, which are more prevalent in the southern hemisphere."
The biggest killer of stranded whales was stress.
"Pilot whales are very sensitive to stress and will need to be released in calm waters," the expert said.
Pilot whales were believed to be notorious for stranding themselves on beaches. The phenomenon is more common along the Australian and New Zealand coastlines.
Long-finned pilot whales can reach over six metres in length, and can weigh more than two tons.
55 killer whales beached
The department of environmental affairs' oceans and coast branch, which coordinates the rescue of stranded whales and dolphins, was not available for comment.
In 2009, 55 killer whales beached on Kommetjie Long Beach in Cape Town.
Hundreds of volunteers and rescue-workers joined forces and saved about a dozen whales. The others were shot. – Sapa