All appointments for Thursday at the vaccination center in Tuebingen were canceled after the site was swamped by torrential rain late Wednesday.
Police said five people were injured in the nearby town of Reutlingen after they were struck and injured by hail the size of tennis balls.
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.
The neighboring Czech Republic and Switzerland were also affected by the heavy rain, with some roads and train tracks made impassable by floodwater.