About 150 of the animals were found beached at Hamelin Bay, about 300km (180 miles) south of Perth.
Their discovery by a local fisherman on Friday prompted a major rescue effort to return them to deeper waters.
However, by nightfall, more than 140 of the whales had died, with deteriorating weather conditions and the threat of frenzied sharks impeding efforts.
More than 100 volunteers, wildlife personnel and others came to the aid of the beached short-finned pilot whales, a species known to strand en masse.
"I've never seen anything like it, seen so many whales beached like this," one tourist told the Associated Press news agency.
"Unfortunately, most of the whales beached themselves on dry land overnight [on Thursday] and have not survived," Parks and Wildlife Service spokesperson Jeremy Chick said in a statement.
Short-finned pilot whales usually measure up to 5m (16ft) and are found in tropical and sub-tropical waters, according to officials.
The rocky beach terrain, dead whales surrounding the survivors and rough seas were challenging factors in moving the surviving whales, officials said.
Mr Chick said there was a risk the surviving whales might come back into shore and re-strand.
"This has often been the case in previous mass strandings," he added.