The former special forces commander, thought to be in his early 40s, faced eight other candidates in a fragmented field with no strong challenger. Ousted President Alpha Conde and longtime opposition leader Cellou Dalein Diallo remain in exile.
Vote counting began after polling stations in Conakry closed at the scheduled time, a Reuters journalist said. There were no major disturbances reported.
Turnout appeared tepid in the capital Conakry as some voters described the election as a foregone conclusion.
"The most important thing is that the country returns to normal. I'm pragmatic. I voted for the one who is in office and who ensures the continuity of the state," shopkeeper Moussa Kaba told Reuters.
Doumbouya, wearing a white robe and sunglasses and accompanied by his wife, waved to crowds as he arrived to vote at a polling station in Conakry flanked by dozens of armed commandos.
Provisional results are expected in two to three days.
Guinea holds the world's largest bauxite reserves and the richest untapped iron ore deposit at Simandou, officially launched last month after years of delay.
Doumbouya has claimed credit for pushing the project forward and ensuring Guinea benefits from its output. His government this year also revoked the licence of Emirates Global Aluminium's subsidiary Guinea Alumina Corporation following a refinery dispute, transferring the unit's assets to a state-owned firm.
The turn toward resource nationalism - echoed in Mali, Burkina Faso and Niger - has boosted his popularity, as has his relative youth in a country where the median age is about 19.
"For us young people, Doumbouya represents the opportunity to send the old political class into retirement," said Mohamed Kaba, a mechanic in Conakry. "There is a lot of corruption right now, but I hope these things will be sorted out."
If elected, Doumbouya "will likely utilise his position to further entrench his power and that of the military over Guinea", said Benedict Manzin, lead Middle East and Africa analyst at risk consultancy Sibylline.
Official results showed turnout in the ballot was 92 per cent, though opposition figures disputed that.
Political debate has been muted under Doumbouya. Civil society groups accuse his government of banning protests, curbing press freedom and restricting opposition activity.
The campaign period "has been severely restricted, marked by intimidation of opposition actors, apparently politically motivated enforced disappearances, and constraints on media freedom," UN rights chief Volker Turk said.
The government did not respond to a request for comment.
