The changes to the Earth's waters were caused by a rash of volcanic activity, wiping out more than 90 per cent of life in the oceans and two-thirds of land animals, said the authors of the study in the journal Science.
The oceans absorbed huge amounts of carbon dioxide from the volcanic eruptions, making the water more acidic and less friendly to fragile life forms.
Back then, the ocean absorbed carbon at a similar rate as today, but it persisted over the course of 10,000 years, said the report, which is based on the study of rocks unearthed in the United Arab Emirates.
"Scientists have long suspected that an ocean acidification event occurred during the greatest mass extinction of all time, but direct evidence has been lacking until now," said Matthew Clarkson of the University of Edinburgh's School of GeoSciences.
"This is a worrying finding, considering that we can already see an increase in ocean acidity today that is the result of human carbon emissions.