Emergency services said most of the serious injuries were of pedestrians or drivers struck by falling trees and flying branches. Many roads had to be closed due to flooding.
In the Karlsruhe area in the south-western state of the Baden-Württemberg alone, emergency services responded to 650 calls in the space of just two hours. One driver narrowly escaped injury when her car was struck by a children's trampoline which had been blown over a garden wall.
In Bavaria, a quad driver suffered serious head wounds when he was hit by a branch while two men who were struck by lightning escaped with relatively minor injuries.
And in Münster in North Rhine-Westphalia, an 80-year-old man died while battling water which had flooded his basement. Further east in Bielefeld, seven cars got stuck in a flooded underpass. One woman was rescued by boat from the roof of her car.
In Berlin, a suburban commuter train was derailed when it hit a tree which had collapsed onto the tracks. More than 1,000 fire fighters worked throughout the night in the capital.
The German Weather Service (DWD) had even issued a tornado alert which stayed in effect until Friday morning, by which time the situation had calmed.
The storm came after the country experienced two very hot days, with temperatures of more than 35 degrees. The coming few days are expected to be cooler, with temperatures in the mid-twenties, with a further cooling expected early next week.