The German Weather Service (DWD) called off its storm warning for hurricane-force winds of up to 120 kilometres per hour in most places, but cities above 1,000 metres were still on alert after several casualties across the country.
In Lower Saxony a 46-year-old man died after colliding with a tree when his car was blown from the roadway, police said.
A 74-year-old German motorist was killed and his wife injured when a tree came crashing down on their car in the Black Forest. Falling trees also killed a woman jogging in the western town of Bergheim and a 69-year-old man walking in a forest west of Frankfurt, police said.
Media reports on Monday also said that a two-year-old boy drowned near Frankfurt after a gust of wind blew him into a river.
Several motorists were hurt as the deadly tempest made its way through Germany, including at Uckerath, south of Cologne, where two motorists were injured by trees falling onto the road, police said.
In the western city of Karlsruhe, several policemen were slightly injured when a tree fell on their truck outside a stadium during a football match.
On Sunday, trains had been cancelled in the states of Rhineland-Palatinate, Saarland, North Rhine-Westphalia, and in Hesse, while there were also problems in Saxony-Anhalt, Thuringia and Saxony.
By Monday morning the main rail corridors were all reportedly free from storm disruptions, though delays on regional trains were expected in the state of North Rhine-Westphalia where the storm was at its strongest on Sunday.
Meanwhile officials reopened the Frankfurt Airport rail station, which was closed on Sunday as a safety precaution due to the weather. Airlines there were forced to cancel some 250 flights during the storm, while the nearby A3 motorway was also briefly closed.
Traffic in Frankfurt and Cologne was also reportedly on time, though commuter train lines between Essen and Düsseldorf, and Koblenz and Trier were still delayed.
The storm sparked some 1,700 emergency calls in the district of Arnsberg in North Rhine-Westphalia before 9 pm on Sunday, and a loss of power to about 70 communities in the Eifel region.
Thirty roads in the county of Trier-Saarburg were reportedly impassable due to falling trees during the violent storm.
Dubbed "Xynthia," the Atlantic storm has already travelled across swathes of Western Europe, killing at least 54 people amid gusts of up to 150 kilometres per hour and eight-metre (26 foot) waves.
The violent weather has also left more than a million households without power across the continent.