A 50-year-old man was killed when his car was struck by a tree in the town of Uelzen in Lower Saxony, as the German weather service DWD confirmed that a tornado had caused widespread damage across northern Germany.
A cyclist was also severely injured by another tree nearby as the atypical weather pattern hit the region.
Meanwhile, an 83-year-old woman died at Gifhorn, also in Lower Saxony, after her car hit a tree that had been blown across the street in strong gales, police said.
The fire department was called to help in 250 different incidents in and around the major port city of Hamburg, while the eastern city of Magdeburg lost power in some areas. There were also reports of livestock being killed in weather-related incidents in some rural areas.
Music fans, meanwhile, had to seek shelter at the venue of a music festival near the city of Bremen that, ironically, is named "Hurricane."
In Hannover, strong storms interrupted an open-air concert by the US rock band Guns N' Roses. Some 70,000 fans were evacuated from the venue and sheltered in a nearby exhibition center. The band later returned to the stage, only finishing their set at around 1 a.m. local time (2300 UTC).
German rail operator Deutsche Bahn has had to shut down several lines in the north of the country after strong winds blew trees and branches onto the tracks.
Deutsche Bahn said on Twitter that some of its busiest routes connecting Hamburg with Berlin, Hanover and Wolfsburg would remain closed until the tracks were cleared.
Commuter trains in northern Germany were also affected by the shift in weather.
Damage to a rail line between the towns of Bielefeld and Gütersloh stranded a train en route from Berlin to Düsseldorf at around 3 a.m. It was later towed away by a diesel locomotive.
Some planes departing overnight from Berlin were grounded at both of the capital's airports amid heavy rain. Those stranded at Tegel and Schönefeld airport were given blankets and water, while camper beds were also set up.
At Schönefeld Airport normal service was expected to resume at around 9 a.m. local time. However, a speaker for the airport warned of potential further delays and urged travelers to check the status of their flight before departing for the airport.
The DWD withdrew several of its earlier weather warnings for Friday, indicating that the threat of more gale-force winds and strong rains in northern Germany had passed.
Only parts of Germany south of the Danube river were expected to see thunderstorms and potential hail, a DWD spokesperson said.
Temperatures were also expected to drop on Friday, down to around 20 C (68 F) in the north and around the Baltic Sea and 25 C in the middle of the country. The southern city of Freiburg was expected to see the highest temperatures nationwide with 33 C.
ss, dm/sms (AP, AFP, dpa)