The freak weather brought havoc to the northern city of Hamburg on Monday, tearing the roofs off houses and overturning cars.
The southern district of Harburg was the hardest hit by the violent storm, which knocked down three cranes at a construction site, killing two operators, a police spokeswoman said. Two other people at the site suffered injuries, she said.
The whirlwind overturned several cars and trucks and one company building had its roof stripped off, local fire services said.
Damage to power masts left parts of the city, including a hospital, without electricity.
The tornado caused serious traffic jams in the area, as well as disruptions to rail services. Police said it was too early to estimate the cost of the damage.
In June 2004, two villages in eastern Germany suffered extensive damage when a tornado tore through them, wrecking houses and leaving hundreds of people with no power.