These downpours were also fed by a conveyor belt of rain that linked up with Hurricane Leslie racing towards Portugal.
Spain was also expected to be hit by the severe weather, dubbed a "zombie" storm because it first formed on 23 September and has meandered through the Atlantic Ocean for weeks.
Forecasters said that portions of Portugal will experience near hurricane-force winds.
Leslie caused a lot of tree damage in the Portuguese seaside town of Figueira da Foz.
Portuguese capital Lisbon and the nearby Setubal, the central Leiria and Santarem as well as Coimbra, Aveiro, Porto, Braga, Viana do Castelo, Vila Real, Castelo Branco, Viseu and Guarda in the north are districts under red warning, according to IPMA.
More than 300,000 homes lost electricity as the storm passed, said Belo Costa, commander at the Civil Protection Agency.
More than 200 power lines were affected by the storm, according to reports from power authority EDP.More news: Ariana Grande & Pete Davidson Reportedly Split, End Engagement
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Maritime authorities advised fishermen at sea to return to the nearest port and Portugal's TAP airline cancelled seven flights to and from Lisbon.
Power was being restored across the north and centre of the country during the morning.
He said that intense wind and rainy periods are still to be expected on Monday and that there are trees and infrastructure that suffered damages during the storm that may still fall.
The Category 1 storm was 500 kilometres (310 miles) southwest of Lisbon, the U.S. National Hurricane Center in Miami said.
It is rare for an Atlantic hurricane to hit the Iberian peninsula as only five have been recorded.
Hurricane Leslie is forecast to weaken slightly as it moves east toward the Iberian Peninsula on Saturday, the National Hurricane Center (NHC) said.