Polls project Subianto -- a military chief during the Suharto dictatorship a generation ago -- to secure a majority and replace popular outgoing president Joko Widodo, who observers claim indirectly supported his campaign.
The 72-year-old is the clear favourite after a campaign mixing populist rhetoric with pledges to continue the policies of Widodo, who has presided over steady economic growth but reached the constitutional two-term limit.
"The hope is to win," Subianto told reporters before voting in the city of Bogor.
"Come to the voting station... cast your votes according to your conscience."
Nearly 205 million people were eligible to vote for Subianto or his rivals -- former Jakarta governor Anies Baswedan and former Central Java governor Ganjar Pranowo -- in what is just the fifth presidential election since the end of Suharto's dictatorship in 1998.
Polls opened at 7:00 am (2200 GMT) in the easternmost region of Papua and closed at 01:00 pm (0600 GMT) at the other end of the country in jungle-clad Sumatra.
A logistical feat involving more than 800,000 polling stations and 20,000 seats up for grabs saw planes, helicopters, speedboats and even cows used to cart ballots around the sprawling archipelago of nearly 280 million people.
In Papua's Timika city, officials inspected makeshift polling stations built from logs, metal sheets and palm leaves as voters arrived to eye candidate lists.
In the capital Jakarta, a thunderstorm deluged 34 polling stations, according to the city's disaster mitigation agency.
Workers wearing shirts that read "not voting is not an option" relocated some stations where ballot boxes had been wrapped in plastic, while others used pumps to drain floodwater.
Official results are not expected until March, but so-called quick counts from government-approved pollsters -- shown to be reliable in the past -- are expected to give an indication of the winner later Wednesday.
Consultant Debbie Sianturi was one of those determined to vote.
"I want to have a leader that will continue the democracy," the 57-year-old said.
Another said Subianto's experience made him a popular candidate.
"He has a military background, so I think he will be a decisive leader," said Afhary Firnanda, a 28-year-old office worker in Jakarta.
Election commissioner Idham Kholik told AFP all voters should be allowed to cast their ballots if large queues remained when polls closed.
Subianto needs to claim more than 50 percent of the overall vote and at least a fifth of ballots cast in over half the country's 38 provinces to secure the presidency.
If he falls short, a second-round vote will be held in June.
Baswedan, seen as the favourite to challenge Subianto in that event, told supporters to help ensure a fair vote in the graft-riddled country, where voters dip their fingers in halal ink to prevent double voting.
"Come back to the voting station, monitor the vote count," he told reporters.
Pranowo, who entered election day last in the polls after once being the front-runner, said he hoped for a clean election.
"Today is the best time for all to return to the good path of democracy," he told reporters.
Another key factor in Subianto's popularity is having Widodo's eldest son, 36-year-old Gibran Rakabuming Raka, as his vice presidential running mate, a move that has raised eyebrows.
In October, Indonesia's then-chief justice, who is Widodo's brother-in-law, changed the rules that had barred candidates below the age of 40 from running for high office.
Widodo enjoys near-record approval ratings after two terms of solid economic growth and relatively stable politics in the nation's young democracy.
But some legal experts and rights groups have accused Widodo of improperly using government funds to support Subianto.
Subianto and his aides have rejected accusations of impropriety.
Subianto was dismissed from the military in 1998 over accusations he ordered the abduction of democracy activists at the end of Suharto's rule, but he denied the accusations and was never charged.
He has since rehabilitated his image, thanks in part to a savvy social media campaign targeting Indonesia's youth that portrayed him as a "cuddly grandpa".
But rights groups have expressed alarm that he could roll back hard-won democratic freedoms, pointing to the alleged disappearances.
"We've been always worried about his commitment towards democracy," said Yoes Kenawas, a researcher at Jakarta-based Atma Jaya Catholic University.
"If he wins, those questions will always linger."
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