At 39, the former investment banker will be the country's youngest-ever leader and faces a huge challenge to heal a fractured and demoralised country.
The vicious election campaign has exposed deep economic and social divisions, as well as tensions around identity and immigration.
"A new chapter in our long history begins tonight. I want it to be one of hope and renewed confidence," Macron told AFP in a call shortly after results were released.
Unknown three years ago, Macron is now poised to become one of Europe's most powerful leaders, bringing with him a hugely ambitious agenda of political and economic reform for France and the European Union.
The result will resonate worldwide and particularly in Brussels and Berlin where leaders will breathe a sigh of relief that Le Pen's anti-EU, anti-globalisation programme has been defeated.
German Chancellor Angela Merkel's spokesman said it was a "victory for a strong and united Europe", while EU Commission President Jean-Claude Juncker said French voters had chosen a "European future."
"France is sending... An incredible message of hope to the world," veteran centrist Francois Bayrou, an ally of Macron, told France 2 television. "Anyone who bet on this has probably made a fortune."
Le Pen, 48, had portrayed the ballot as a contest between Macron and the "globalists" -- in favour of open trade, immigration and shared sovereignty -- and her "patriotic" vision of strong borders and national identities.
Macron will now face huge challenges as he attempts to enact his domestic agenda of cutting state spending, easing labour laws, boosting education in deprived areas and extending new protections to the self-employed.
The philosophy and literature lover is inexperienced, has no political party and must try to fashion a working parliamentary majority after legislative elections next month.
His En Marche movement -- "neither of the left, nor right" -- has vowed to field candidates in all 577 constituencies, with half of them women and half of them newcomers to politics.
Many analysts are sceptical about Macron's ability to win a majority with En Marche candidates alone, meaning he might have to form a coalition of lawmakers committed to his agenda.
Furthermore, his economic agenda, particularly plans to weaken labour regulations to fight stubbornly high unemployment, are likely to face fierce resistance from trade unions and his leftist opponents.
He also inherits a country which is still in a state of emergency following a string of Islamist-inspired attacks since 2015 that have killed more than 230 people.
Hundreds of thousands of emails and documents stolen from his campaign were dumped online on Friday and then spread by anti-secrecy group WikiLeaks, leading the candidate to call it an attempt at "democratic destabilisation."
France's election authority said publishing the documents could be a criminal offence, a warning flouted by Macron's opponents and far-right activists online.
It was the latest twist in an election that has consistently wrong-footed observers as angry voters chose to eject establishment figures, including one-time favourite Francois Fillon, a rightwing ex-prime minister.
In the first round of the presidential election on April 23, Macron topped the vote with 24.01 per cent, followed by Le Pen on 21.30 per cent, in a crowded field of 11 candidates.
The results revealed Macron was favoured among wealthier, better educated citizens in cities, while Le Pen drew support in the countryside as well as poverty-hit areas in the south and rustbelt northeast.
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