With this victory, Macron, 39, who was unknown three years ago and mocked by his country's politicians and media when he announced his presidential bid, became the youngest president of France's Fifth Republic.
Interior Ministry said with all ballots counted early Monday, Macron won 66.1 percent of the vote, whereas Le Pen got 33.9 percent.
The turnout was 74.56 percent, the lowest in 40 years, while the abstention rate was the highest since 1969 when a record 31.1 percent abstained from voting for either of the two centre-right candidates: Georges Pompidou and Alain Poher.
Blank or spoiled votes also reached an absolute record of about 11.47 percent, corresponding to more than 4 million, or 8.56 percent of all registered voters.
Despite the defeat, the far-right has marked a new record performance that reflects the deep divisions in France the president-elect must attempt to reduce.
In her conceding speech, Le Pen said the National Front was now the country's leading opposition party, and pledged to make a "profound reform" in the party in order to create "a new political force".
In his address to thousands of his supporters at the celebration event in the grand courtyard of the Louvre Museum, Macron vowed to fight against the divisions and said he "will do everything to make sure you never have reason again to vote for extremes," in reference to the landmark results of his far-right rival.
Le Pen had nearly 11 million votes, double her father's score in 2002 when he was beaten by conservative candidate Jacques Chirac in the run-off.
Macron is now faced with the hard and urgent task of uniting a divided nation living under a state of emergency, as well as finding solutions to reduce a record high unemployment in a suffering economy.
In order to fulfill this goal, he first needs to secure a parliamentary majority for his political movement 'En Marche!' (On the move!) in next month's legislative elections.
He also has to appoint a prime minister and form a government as soon as possible. He already said on Friday that he had decided who would be his prime minister if he won Sunday’s vote, but refused to reveal the name.
His campaign team said Sunday that Macron "will name his Prime Minister next Sunday when he assumes power".
Macron, a former investment banker, served as top adviser on economic issues of outgoing president Francois Hollande from 2012 to 2014, then as economy minister in his Socialist government for two years.
He later founded his own political movement 'En Marche!' in April last year.
VE Day celebrations
Later on Monday, Macron participated, along with Hollande, in a ceremony marking the 72nd anniversary of the end of the World War II, known as the Victory in Europe Day or VE Day.
"This year I wanted Emmanuel Macron to be here with me, at my side, so that the flame could be passed to him," Hollande told France 2 about standing alongside Macron.
The outgoing president said it was an emotional moment for him to be at the commemorations with Macron, who was his former economy adviser, and then minister.
"I feel very emotional being here. And then, to speak honestly, [about] showing Emmanuel Macron the path to take," he said.
The ceremony marks the first time the two have been in public together since Macron’s resignation last August.
Speaking about Macron's victory, Hollande said he was not planning to "profit" from it and "it is the French people who chose him".
"He [Macron] is the president and it’s up to him now, bolstered by the experience he had with me, to continue on his path,” Hollande said, adding: "I wish him every success. And he knows that if he has any need for some information, or advice, I will always be at his side."
Hollande confirmed he would formally hand over the power to Macron on Sunday.
"On [next] Monday, I will be a [regular] citizen of France and I will be attentive to the situation of my country and I will be ready to help with any requests people ask of me."
The official results of the run-off round will be announced Wednesday by the president of the Constitutional Council, Laurent Fabius.