The divisive election to choose the next president has turned the country’s politics upside down, with neither of the two mainstream centre-right and centre-left parties that have governed France since the Second World War making it to the runoff.
Independent centrist Mr Macron topped 66 per cent of the vote with the interior ministry having counted 99 per cent of the country's 47 million registered votes counted. He has become the youngest president of the Fifth Republic at the age of 39.
A record 11.5 per cent of votes cast were either blank or spoiled, while a near-record total of 25.38 per cent of the registered voters abstained, the official figures showed.
The first projections from polling agencies had suggested Mr Macron would beat Ms Le Pen - who temporarily stepped down as leader of her Front National (FN) party ahead of the final round of voting - by about 65 per cent to 35 per cent.
Mr Macron was out-going President Francois Hollande’s former Finance Minister, before quitting to found his own centre-left En Marche! movement and run for president himself.
He had enjoyed growing support from voters and gained high-profile backers, including the former Prime Minister Manuel Valls.
Outgoing President François Hollande congratulated Mr Macron and said the result showed the French people wanted to unite around the "values of the republic".
Mr Macron told AFP: "A new page in our history is turning tonight", one he wishes to be "the one of hope and rebound trust".
Ms Le Pen called her opponent to wish him success in dealing with the "challenges" facing the country, following the early results.
She claimed the vote was a “historic, massive result” for the French far-right, telling supporters that the FN "must renew itself to live up to this historic opportunity and the expectation of French people."
In a campaign that has seen favourites drop out of the race one after the other, Ms Le Pen, who wanted to clamp down on immigration and take France out of the European Union, came closer to elected power than any far right candidate has been in Western Europe since the 1930s.
Ms Le Pen picked up a record 7.6 million votes in the first round of the election. This is the strongest ever result for a far-right candidate and 2.8 million more than her father, Jean-Marie Le Pen, got when he made it through the first round of the presidential election in 2002.
That year, Jean-Marie was crushed by his opponent, Jacques Chirac, who received 82 per cent of the vote in the runoff. This is nearly 20 per cent more than the result for Mr Macron, showing that such strong opposition to the FN is fading among the electorate.
Ms Le Pen's niece, Marion Marechal-Le Pen, told the L'Opinion daily that a 40 per cent score would already be "a huge victory" for the FN, and while Marine Le Pen could not reach that number - it was still a record performance for the party.
The voting concluded on Sunday amid high security.
Louvre grounds, where French presidential candidate and favourite Emmanuel Macron was planning to celebrate his possible victory later in the evening, was evacuated for security checks after a suspicious bag was found.
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