Two people were electrocuted and two -- including a child -- drowned trying to cross a raging stream to safety, the state emergency agency said in a report.
Lidia has been wreaking havoc up and down Mexico's Pacific coast and as far inland as Mexico City since Wednesday.
It made landfall early Friday and is slowly churning across the peninsula, which is home to the swank strip of beach resorts known as Los Cabos.
Lidia has maximum sustained winds of 95 kilometers (60 miles) per hour and is expected to dump 15 to 30 centimeters (six to 12 inches) of rain on the Baja California -- up to 50 centimeters in some areas -- before exiting the peninsula late Saturday and weakening, according to the US National Hurricane Center's 2100 GMT update.
Tourists were evacuated from the resort towns of Cabo San Lucas and San Jose del Cabo and taken to shelters set up by the authorities.
Some 1,000 people sought refuge in shelters in the state capital La Paz and another 3,000 in Los Cabos.
In Mexico City, a huge downpour caused by Lidia forced the international airport to cancel 18 flights and divert 40 arriving planes on Wednesday night -- including one carrying Nobel Peace Prize winner Malala Yousafzai, who was on her way to give a speech but found herself temporarily diverted to Cancun, some 1,600 kilometers (1,000 miles) away.
On Thursday, the rains triggered a large cave-in on a central street in the capital, opening a gaping hole at least 10 meters (33 feet) wide and seven meters deep.
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