These downpours were also fed by a conveyor belt of rain that linked up with Hurricane Leslie racing towards Portugal. However, the commander of civil defense White Luis Costa said that "the biggest danger behind".
Maximum sustained winds in the former Category 1 hurricane decreased to 70 miles per hour (110 kph) as the storm neared Portugal's west coast, the U.S National Hurricane Center in Miami said.
Winds of 110mph were recorded as the hurricane, which weakened slightly into a post-tropical cyclone, swept into northern and central Portugal overnight, with officials warning people not to venture outdoors.
Portugal's weather service issued red warnings - its highest level- for high winds or risky coastal conditions for 13 of its 18 mainland districts, including Lisbon, the capital. After the storm passed, trees and power lines blocked sidewalks.
"Leslie" called one of the most powerful storms ever experienced in Portugal.
State broadcaster RTP said Leslie's wind speeds reached 170kmh in the coastal town of Figueira da Foz, 200km north of Lisbon.
In Portugal cancelled three dozen flights and closed several highways and Railways.
The Category 1 storm was 500 kilometres (310 miles) southwest of Lisbon, the U.S. National Hurricane Center in Miami said.
Over the past 176 years, only Hurricane Vince has made landfall on the Iberian peninsula, hitting southern Spain in 2005, according to weather records.
On the forecast track, the center of Leslie will pass north of Madeira Island on Saturday, and approach the southwestern portion of the Iberian Peninsula on Saturday night, and move inland over portions of the Iberian Peninsula on Sunday.
Earlier this week, 12 people died in the flooding on Mallorca in the Mediterranean.