Inamine is a strong opponent of the joint US-Japan project to move the US Marines’ Futenma Air Station from an urban area in the south of Okinawa to Nago, which lies on the coast.
Toguchi has not openly discussed his position on the relocation plan, running instead on a pledge to boost the city’s tourism.
Local media had dubbed the race a "proxy war" between Okinawa governor Takeshi Onaga, who is opposed to the US base plan, and Abe’s government, with the vote seen as a precursor to Okinawa’s gubernatorial election later this year.
Abe welcomed Toguchi’s victory in comments on Monday.
"I’m really grateful for the victory and I appreciate Nago citizens for electing him," he told reporters.
"On the base issue, I will proceed with the plan with the understanding of the citizens," Abe said.
Japan and the US agreed in 1996 to move the base from the town of Ginowan to the Nago coast but the plan has been stalled due to opposition from many residents of Okinawa, which hosts the bulk of some 47,000 US troops based in Japan.
Opponents of the base want it relocated out of Okinawa altogether.
Several recent incidents have fuelled local opposition, including an emergency landing by an American military helicopter two weeks ago.
A series of crimes including rapes, assaults, hit-and-run and drink-driving accidents by US personnel have also triggered protests on Okinawa, and are a frequent irritant in relations between close security allies Japan and the US.
Okinawa was the site of a major World War II battle that was followed by a 27-year US occupation of the island, and it would serve as a launchpad for any American military activity in Asia.
In Sunday’s election, Toguchi won 20,389 votes to beat Inamine, who received 16,931 votes. VNS