Polling day follows a rollercoaster campaign marked by scandal, repeated surprises and a last-minute hacking attack targeting Macron, a 39-year-old former investment banker who has never held elected office.
The run-off vote pits the pro-Europe, pro-business Macron against anti-immigration, anti-EU Le Pen, two radically different visions that underline a split in Western democracies.
Le Pen, 48, has portrayed the ballot as a contest between the "globalists" represented by her rival -- those in favour of open trade, immigration and shared sovereignty -- against the "nationalists" who defend strong borders and national identities
"The world is watching," said 32-year-old marketing worker Marie Piot as she voted in a working-class part of northwest Paris.
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"After Brexit and Trump, it's as if we are the last bastion of the Enlightenment," she said.
Le Pen cast her ballot in her northern stronghold of Henin-Beaumont, where bare-breasted Femen activists climbed scaffolding on a church and unfurled a banner reading: "Power for Marine, despair for Marianne," referring to the symbol of France.
Outgoing Socialist President Francois Hollande, who decided in December against seeking re-election, cast his ballot in his former electoral fiefdom of Tulle, in central France.
Hollande, who plucked Macron from virtual obscurity to name him economy minister in 2014, said voting "is always an important, significant act, heavy with consequences".
Turnout was 28.2 per cent at midday, down from 30.7 percent at the same point in the last presidential election in 2012, the interior ministry said.
Most polling stations close at 1700 GMT, but those in big cities will stay open an hour longer. First estimated results will be published at 1800 GMT.
Hundreds of thousands of emails and documents stolen from the Macron campaign were dumped online and then spread by anti-secrecy group WikiLeaks, in what the candidate called an attempt at "democratic destabilisation".
France's election authority said publishing the documents could be a criminal offence, a warning heeded by traditional media organisations but flouted by Macron's opponents and far-right activists online.
It is the first time neither of the country's traditional parties has a candidate in the final round of the presidential election under the modern French republic, founded in 1958.
Macron would be France's youngest-ever president and was a virtual unknown before his two-year stint as economy minister, the launchpad for his presidential bid.
He left the Socialist government in August and formed En Marche! (On the Move), a political movement he says is neither of the left nor the right and which has attracted 250,000 members.