"Congratulations to Emmanuel Macron on his big win today as the next president of France. I look very much forward to working with him!" Trump tweeted after the poll results came in.
The White House later issued a statement congratulating the 39-year-old pro-European Union Macron, who will become France's youngest-ever leader.
"We congratulate President-elect Macron and the people of France on their successful presidential election," said Press Secretary Sean Spicer. "We look forward to working with the new president and continuing our close cooperation with the French government," Spicer said according to the statement.
Le Pen's decisive defeat, with just estimated 35 per cent votes, has put Trump in a slightly tricky spot after he had indicated support for the far-right leader ahead of the first roud of the presidential polls.
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Trump had tweeted that Le Pen could benefit from the security fears in France over intermittent terrorist attacks.
He had said a deadly attack against a police officer in the Champs-Elysee in Paris would have a "big effect" on the presidential election and praised Le Pen, calling her "the strongest on what's been going on in France."
His predecessor Barack Obama had released a video last week backing Macron.
Yesterday, American lawmakers also joined the White House in congratulating Macron, a former investment banker.
"The French people have chosen hope over fear, chosen to look forward rather than backward. They have rejected the kind of divisive campaigning, assisted by fake news and Russian hacks, that propelled Donald Trump into office in our count," said House Democratic Whip Steny H Hoyer.
"They have struck a blow for inclusive, tolerant democracy against the tide of extremism and xenophobia."
The results, Cardin said, sent the "strongest possible" message to Russian President Vladimir Putin that his worldview has once again been rejected by European voters.
"In spite of allegations of Russian interference similar to that seen in our country last year, democratic institutions across France proved resilient," he said.