According to local media, the conditions were intense enough to produce a damaging tornado in the town of Dolores.
A 67 year-old man died after being hit by lightning in a nearby community, along with two workers at a rock quarry near the Brazilian border.
At the height of the storm, winds topped 160 km/h, damaging at least sixty homes, downing trees and causing widespread power outages.
The violent storms began on Thursday and are expected to fizzle out by the weekend.
With files from Reuters