A White House statement congratulated "Macron and the people of France on their successful presidential election".
Presidential election polls hailed Macron as the victor in Sunday's vote shortly after polling stations closed at 8pm.
But Macron left the position to found his own political movement past year, and has distanced himself from his former mentor.
On the campaign trail this spring, Le Pen's rhetoric had often echoed Trump's, with vows to put "France first" and to defend "the forgotten France".
She was able to vote without any incident after feminist activists were briefly detained a couple of hours earlier for hanging a big anti-Le Pen banner from a church.
The two parties that have run France for almost 60 years have lost power and the next president of France will either be far right nationalist or a 39-year-old politician who has never held public office. The race here also focused on the deeper question of what it means to be French. The 39-year-old independent centrist beats far-right rival Marine Le Pen to get the keys to the Elysee Palace.
The Socialist candidate, Benoit Hamon, was eliminated in the election's first round after receiving some 6 percent of the vote.
Despite her electoral defeat, Le Pen's National Front party has achieved success by moving into the mainstream of French politics.
As New York contributor Heather Hurlburt highlights in her sobering post-election warning to France's liberals, both abstention and blank-ballot rates among French voters reached historic highs on Sunday, and the politically inexperienced Macron now has to try to cajole political unity within France if he hopes to have any real power moving forward.
"Marine Le Pen has tried to put a positive spin on her loss tonight", said Al Jazeera's senior political analyst Marwan Bishara.
Pollsters project Mr Macron won 65% of the vote to make him France's youngest president in history.
The ex-investment banker's programme pledges to cut state spending, ease labour laws, boost education in deprived areas and extend new protections to the self-employed.
A European integrationist and pro-Nato, he is orthodox in foreign and defence policy and shows no sign of wishing to change France's traditional alliances or re-shape its military and peace-keeping roles in the Middle East and Africa.
French presidential election candidates Marine Le Pen and Emmanuel Macron stand side by side.
The eyes of the world have been on the French election, in part because Macron is a political novice. Leaders from across Europe also sent messages of congratulation.