A man who was in the same boat was able to swim to another vessel from where he fired "two flares", Joanna Matta, police spokeswoman for the canton (region) of Geneva, told AFP.
The man told officers that the woman had been "passing through Geneva" and that the storm had taken them "by surprise", Matta said.
Three police boats and emergency services rushed to the scene. Police divers later retrieved the woman's body from the lake.
The victim, whose nationality remains unknown, was then taken to a hospital in Geneva where she was declared dead.
In a separate incident, the storm also damaged some of the 465 boats taking part in the 81st edition of the Bol d'Or, an annual regatta on Lake Geneva, the event's press service said.
Heavy rain and strong winds lashed the participants on Saturday afternoon, causing boats to capsize although nobody was injured.
However, the storm broke the mast of the ultra-fast "Real Team" catamaran, which had been in the lead and was forced to pull out of the race.
The bad weather struck western Switzerland on Saturday afternoon, bringing hail and winds reaching up to 110 kilometres (70 miles) per hour, according to the national forecaster MeteoSwiss.
In the neighbouring French region of Haute-Savoie the storm also caused damage and left a 51-year-old German tourist dead after a tree came down at a campsite.