The whirlwind ripped off roofs and overturned at least 10 cars, with witnesses describing the scene as “apocalyptic”.
A hospital helicopter from nearby island of Lampedusa was initially unable to reach the island to provide assistance because of the bad weather.
The dead include a 47-year-old off-duty fireman and an 86-year-old pensioner, both of whom were driving when the tornado struck, according to Italian news agency ANSA.
According to testimonies, the tornado ripped down a road along the Campobello coastline in seconds.
Photographs posted on social networks show cars thrown against houses, other vehicles badly damaged or flipped, and flooded streets.
Closer to North Africa than Italy, Pantelleria is famed for its hot spring waters and attracts thousands of tourists every year, including Sting and Giorgio Armani, who owns a luxury villa there.
