All appointments for Thursday at the vaccination center in Tuebingen were canceled after torrential rain late Wednesday.
Police said five people were injured in the nearby town of Reutlingen after they were struck and injured by large hailstones.
Firefighters were out in force across the region pumping water out of flooded basements and removing toppled trees from roads, police said.
The downpour also drenched players and spectators at the Germany-Hungary Euro 2020 match held in Munich on Wednesday evening, forcing some public viewings to be abandoned. The game ended in a tie.
In the neighboring Czech Republic, a rare tornado hit towns and villages in southeast part of the country, injuring some 150 people and damaging hundreds of houses. Some 200 police officers have been deployed in the region to help the rescue workers.
Earlier in the day, thunderstorms before dawn Thursday left some 100,000 households in central and southern areas of the Czech Republic without electricity, while fallen trees blocked the tracks on some 30 train routes. About 45,000 households were still without power later Thursday.