The ruinous typhoon threatened to thwart the election from taking place but the vote successfully went ahead with Denny Tamaki elected governor, domestic media reported.
Mr Tamaki, who defeated a candidate backed by Prime Minister Shinzo Abe’s ruling party, ran on an anti-US military presence platform.
The defeated Atsushi Sakima had the support of the Liberal Democratic Party and its coalition partner.
Newly elected governor Mr Tamaki told reporters: “The strong feelings of Takeshi Onaga, risking his life to stop the construction of any more bases, helped bring this victory.”
Mr Tamaki’s words were in reference to Takeshi Onaga, who held the post of Okinawa governor previously and died of pancreatic cancer in August.
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Mr Onaga’s agenda was to remove US military bases off Okinawa.
On the campaign trail, Mr Tamaki had pledged to continue in Mr Onaga’s “spirit”.
Typhoon Trami made landfall in Tokyo on Sunday after it barrelled through Okinawa and Kagoshima Prefecture on Saturday leaving at least 53 injured.
The “very strong” storm caused a deluge of flooding and left a plague of destruction in its wake.
Ahead of Sunday’s election, residents were urged to vote in advance in case the storm prevented them from casting their votes.
But fears the election would not go ahead were allayed as Okinawa’s new governor accepted his new title.
On hearing the news of his election, Mr Tamaki thanked his supporters as his campaign office began cheering and dancing Okinawa-style.
Mr Tamaki’s election – and pledge to honour the “spirit” of his anti-US predecessor – is likely to impact the controversial plan to relocate a US Marine Corps Air Station Futenma in Gionwan to a new offshore facility on the north of the Island.
In a clear indication of his tough stance, during his campaign 58-year-old Tamaki unequivocally declared: “I can clearly state we no longer want in Okinawa the US bases that destroy our peace and destroy our nature.”
The former radio presenter has also vowed to implement policies that care about “the weak”, helping workers, students and those who face discrimination.