The storm came as the city was getting ready to welcome up to a million techno music fans for Saturday's Love Parade, but organisers predicted it would not disrupt festivities.Hurricane-like winds of 150 km (93 miles) an hour uprooted around 1,000 trees in the capital and surrounding region. Streets were strewn with debris, disrupting public transport and causing traffic delays.
Air traffic and rail services were suspended temporarily.
A large tree fell across the route of the annual ravers' day out in the city's central Tiergarten park but organisers said they expected the route to be clear by Saturday and they were not worried about bad weather dampening spirits.
"The weather forecast for the Love Parade is fantastic. The Parade is going to be the calm after the storm," a spokesman said.
Berliners picked their way through fallen branches on suburban roads and central boulevards last week morning after the storm, which saw the biggest deployment of Berlin emergency services in 25 years.
The two children died while camping on an island in Wannsee lake in Berlin, a police spokesman said, while 13 campers were injured, two seriously. The high winds made rescuing the group on the island difficult, he said.
A group of children from New York, all related to firemen killed in the September 11 attacks on the United States, visited the island on Wednesday as part of an exchange programme but were not caught up in the storm, the police spokesman said.
Two men were killed in northern Berlin by falling trees while in the surrounding Brandenburg region, branches and debris killed three people.
Berlin's main Tegel airport was closed to traffic for some time and a Crossair passenger aircraft was forced to make an emergency landing after running out of fuel.
The plane's 20 occupants escaped unharmed after the aircraft landed safely in a former Soviet airfield at Werneuchen in the eastern part of the city.
Dozens of people were reported injured by flying debris and glass overnight and firefighters said they answered over 2,000 emergency calls for assistance.
Bad weather was also reported in other regions. German television said emergency services in Hamburg received around 600 calls for assistance. There were several reports of lightning setting fire to buildings.
(Additional reporting by Katya Andrusz).