Helene weakened to a Category 1 hurricane early on Friday with maximum sustained winds of 75 mph (120 kph), according to the National Hurricane Center (NHC), but it left a deadly trail of destruction in both states.
More than 55 million people in the US have been placed under some form of weather alert.
As of Friday morning, broadcaster ABC reported two deaths in Georgia's Wheeler County, while Florida confirmed one death, after a sign fell on a car on a highway in Tampa City.
The hurricane made landfall in northwestern Florida as a Category 4 storm as forecasters warned that the enormous system could create a "nightmare" storm surge and bring dangerous winds and rain across much of the southeastern US.
Helene was moving rapidly inland after making landfall, with the risk of tornadoes continuing in Florida, Georgia, South Carolina and southern North Carolina, forecasters said.
"Helene continues to produce catastrophic winds that are now pushing into southern Georgia," the NHC said in an update on Friday. "Persons should not leave their shelters and remain in place through the passage of these life-threatening conditions."
Florida state authorities provided buses to evacuate people from the Big Bend area, home to about 832,000 people, and taking them to shelters in the state capital, Tallahassee.
Officials in Florida urged residents to heed mandatory evacuation orders or face life-threatening conditions ahead of the hurricane's landfall.
"EVERYONE along the Florida Big Bend coast is at risk of potentially catastrophic storm surge," the NHC said on social media.
States of emergency were also declared in Virginia and Alabama, as the NHC warned that much of the southeast could experience power outages, toppled trees and intense flooding
In the southern Appalachian mountains, the National Weather Service has warned the region could be hit with landslides and flooding not seen in more than a century.
"This will be one of the most significant weather events to happen in the western portions of the area in the modern era," it said.
Only three Gulf hurricanes since 1988 - Irma in 2017, Wilma in 2005, and Opal in 1995 - have been bigger than Helene's predicted size, according to Colorado State University hurricane researcher Phil Klotzbach, The Associated Press news agency reported.
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