A man in a wheelchair was found dead in a river in the northern city of Hamburg, according to local firefighters.
Witnesses saw him fall into the water and despite a rescue effort that included divers, a boat and a helicopter, he could not be saved.
A pedestrian also died in Hamburg after he was hit by scaffolding that fell from the seventh floor of a building, police said. He was taken to hospital where he later died.
A 53-year-old man was the third person to be killed in the storm after being crushed by a tree near the west German spa town Brilon. The man was working in the forest when a 20-metre tall spruce tree fell on him, local police said.
The first autumn storm of the year also managed to uproot numerous trees across Germany. According to the Deutsche Bahn, trees had to be cleared from tracks and damaged overhead lines had to be repaired.
Hundreds of employees were deployed to repair the damage caused by the storm. Deutsche Bahn also provided stranded passengers with accommodation in Bremen, Dortmund, Hamburg and Hanover; some travellers were given soup and drinks.
A number of fire brigades were deployed in East Frisia and Bremen. Many ferry routes in the North Sea were also cancelled.
Several regions of Germany have issued warnings advising residents to stay home while emergency services clear roads and fix power outages.
Meanwhile on Thursday morning, commuters particularly in rush hour traffic in northern Germany will still be affected by the aftermath of the storm.
According to DB, four track lines in the Hamburg, Kiel and Lubeck area have been suspended and delays on several other train routes could be expected.
The German Weather Service (DWD) also warned that storms in the southwest of Germany could continue on Thursday. In the morning, there could be continuous rainfall with potential flooding in southern Hesse, parts of Baden-Württemberg, Rhineland-Palatinate and Saarland.
In Hamburg as well as in towns along the North Sea, winds of up to 85 kilometres per hour could pass through as well, though diminishing by the evening.
On Friday, thunderstorms and showers may be seen in northwestern Germany. According to DWD, wind speeds are expected to be moderate and will weaken into the weekend.