The vote, seen as crucial for Europe's future, caps a rollercoaster race marked by mudslinging, scandals and a last-minute hacking attack targeting Macron, a 39-year-old former banker who has never held elected office.
The run-off vote pits the pro-Europe, pro-business Macron against the anti-immigration, anti-EU Le Pen, two radically different visions that underline a split in Western democracies.
Turnout at 1500 GMT stood at 65.30 per cent, 6.6 points down on the 2012 presidential election and about four points lower than the April 23 first round, data from the interior ministry showed.
She is hoping to spring a shock win that would resonate as widely as Britain's decision to withdraw from the European Union or the unexpected victory of US President Donald Trump.
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Macron, who topped the first round of the election on April 23, is the runaway favourite however, with polls giving him a lead of more than 20 points over Le Pen.
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.
Both candidates later travelled to Paris to see in the results.
"The world is watching," said 32-year-old marketing worker Marie Piot as she voted in a working-class part of northwest Paris.
"After Brexit and Trump, it's as if we are the last bastion of the Enlightenment," she said.
A spokesman for Macron's En Marche (On The Move) movement said a suspicious package had been found.
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".
The hacking of his campaign was revealed on Friday evening. Paris prosecutors are investigating the attack, a source close to the case said today.
Hundreds of thousands of emails and documents 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.
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 his movement that he says is neither of the left nor the right and which has attracted 250,000 members.
He is also fervently pro-European and wants to re- energise the soon-to-be 27-member European Union, following Britain's referendum vote last June to leave.
National Front leader Le Pen sees herself as part of the same backlash against globalisation that has emerged as a powerful theme in the United States and in recent elections in Britain, Austria and The Netherlands.
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