As the polling stations began to close from 1800 GMT, officials began counting the votes.
By running, the strongman reneged on a pledge not to stand for office and to hand the west African country back to civilian rule by the end of 2024.
Since seizing power in 2021, Doumbouya has cracked down on civil liberties, and protests have been banned while opponents have been arrested, put on trial or driven into exile.
Some 6.8 million people were eligible to choose between the nine approved candidates. Doumbouya, 41, is running as an independent.
Earlier, escorted by dozens of special forces personnel, the junta chief voted with his wife in a central district of the capital Conakry.
Dressed in a boubou and white cap, Doumbouya — who did not hold any rallies during the campaign — greeted supporters but made no statement.
AFP journalists saw a large security presence, including armoured vehicles, patrolling the capital’s streets.
“I am here to fulfil a civic duty,” Colle Camara, a 45-year-old teacher, told AFP, as he cast his ballot in what he hoped would be a “peaceful” election.
Doumbouya looked set to win in the first round of voting, against eight relatively unknown remaining rivals. Provisional results are expected within two days.
The opposition called for a boycott of the vote, in a country rich in minerals but where 52 percent of the population lives in poverty, according to World Bank figures.
UN human rights chief Volker Turk said Friday the campaign had been “marked by intimidation of opposition actors, apparently politically-motivated enforced disappearances, and constraints on media freedom”.
Guinea’s electoral authority put overall voter participation at a provisional 85 percent shortly after voting ended.
Guinea experienced a rare democratic transition with the 2010 election of Alpha Conde, its first freely elected president.
Doumbouya overthrew him in September 2021.
Guinea’s new constitution allowed junta members including Doumbouya to stand for election and lengthened presidential terms from five to seven years, renewable once.
Opposition leader and former prime minister Cellou Dalein Diallo has condemned the vote as “an electoral charade” aimed at giving legitimacy to “the planned confiscation of power”.
He is one of three opposition leaders barred from standing in the vote by the new constitution.