In the Czech Republic, falling trees killed a woman near the central city of Trebic and an elderly man in Jicin northeast of Prague.
A driver died in his car in Poland after crashing into a branch that had fallen on the road near the northwestern city of Szczecin, firefighters said.
The strong winds halted traffic on dozens of railways and several roads across the Czech Republic. Some rivers in the north of the country reached the highest flood-alert levels.
"At present, hundreds of thousands of households are left without power," Sona Holingerova Hendrychova, spokeswoman for the state-run power producer CEZ, said in a statement.
About 200,000 people were also grappling with power outages in western Poland.
In Austria, the organisers cancelled the men's World Cup season-opening giant slalom at Solden scheduled for Sunday.
In Germany, the storms caused flooding in Hamburg, where waters rose up around the city's fishmarket.