They said a 43-year-old man was killed and a 15-year-old girl seriously injured by falling trees during a local festival in the southern town of Forcheim.
A man was also killed when he lost control of the car he was driving during heavy rains in the southwestern state of Baden-Wurttemberg.
In the eastern town of Hohenstein-Ernstthal, 41 people were injured by flying objects at the German motorcyling Grand Prix.
Three men were also injured after being struck by lightning in the southwestern town of Karlsruhe.
High winds, which reached 191 kilometers (118 miles) per hour in the northern Saxony region, downed trees and damaged houses. Heavy rain also forced authorities to close some major roads, while rail services were also affected.
In the southwestern town of Muenstertal, a mini-tornado damaged about 50 houses, 14 of them severely.
In the eastern town of Hohenleipisch-Hochsschwarzwald, some 90 people were forced to spend the night on a high-speed train that was blocked by a mudslide.
Twelve of Germany's 16 states were affected by the bad weather.
The storms also battered neighbouring Switzerland, in particular the cities of Geneva and Basel, but there no reports of casualties or major damage.