A 60-year-old man drowned near the town of Takilsa and another man was found dead in Bir Bouregba, close to the town of Hammamet, interior ministry spokesman Sofiene Zaag told AFP.
Two sisters were swept away as they left work at a factory in Bou Argoub, 28 miles southeast of the capital, the ministry said.
The storm dumped 200 millimetres (7.9 inches) of rain on Nabeul and up to 225 millimetres in the city of Beni Khalled, in the peninsula's centre, according to Tunisia's National Institute of Meteorology.
It was the heaviest rainfall since the institute began keeping records in 1995, it said, adding that it had issued a warning about the storms on Friday.
Videos posted to social networks showed surging waters carrying cars and chunks of road in the north of the peninsula.
Tunisian authorities said they had dispatched police, army and rescue teams to the region on Saturday afternoon, in addition to mobilising ambulances and two helicopters.
Prime Minister Youssef Chahed visited affected areas to meet survivors on Sunday, as authorities took preventative measures in the Sahel region further south in case of further rains.
The sun was out Sunday and receding water levels meant most of the area's roads were passable by car, the interior ministry's Zaag said, although the region's telephone networks were still largely out of service.
Severe thunderstorms have hit Tunisia since the middle of last week, flooding roads and damaging property, sparking anger against the authorities for allegedly failing to maintain drainage systems.
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