One person was killed in Walchsee in the western province of Tyrol after a tree struck their car, local police said.
Further east in Lower Austria, the local fire department announced that another person had been killed in their car by a fallen tree, and two people had also been injured in the storm.
Up to 10,000 homes were without power in Upper Austria, according to the local power company, while elsewhere, fallen trees and broken power lines caused severe disruption.
Roads and sections of motorway also had to be shut down. In Vienna, train services had to be diverted after a crane crashed onto the rails at the Suedbahnhof train station. Nobody was injured, according to police.
Last year, a construction worker was killed in Vienna when his crane fell onto a nearby building during a similar storm.
Winds of up to 190 kilometres per hour hit the Alps and meteorological services warned of avalanches, while in the lowlands winds were expected to reach 135 kilometres per hour.
An Austrian Bundesliga football match between Salzburg and Innsbruch, scheduled for Saturday afternoon was also cancelled due to the storm. An alternative date has not yet been set.