More than 10 million electors didn't vote at all, surpassing the 8.5 million who voted for Mr. Macron and the 7.7 million for Ms. Le Pen.
Le Pen won 21.4 percent of the vote on Sunday to 23.9 percent for Macron, who is now projected to defeat her by a margin of about 20 points in the runoff.
Ms Le Pen has worked to bring in voters from the left and right for several years, cleaning up her party's racist, anti-Semitic image to do so.
"We can not allow the slightest porosity with the Front National", he told Le Monde, warning the party risked foundering in parliamentary elections if it failed to keep its distance from the FN.
While a financial scandal derailed the presidential bid of French conservative Francois Fillon, Le Pen, who is staunchly anti-EU, has so far survived the allegations unscathed.
United Kingdom in a Changing Europe research fellow Matthew Goodwin said in terms of political shocks, a Le Pen win would put Brexit and the election of US President Donald Trump in the shade and pose an "existential" blow to France and Europe.
In a televised speech from the Elysee Palace, Hollande warned that Le Pen's anti-immigrant nationalism would "deeply divide France", which has been under a state of emergency since the 2015 ISIS terror attacks.
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Ms Le Pen announced on Monday she will be temporarily stepping down as leader of the Front National to concentrate on the election campaign and broaden her appeal to less extreme voters.
Le Pen and Macron will face off in a live televised debate on May 3. The far-right Le Pen and centrist Macron both took just under a quarter of the vote in a contest with 11candidates. Speaking from the Elysee presidential palace, Hollande said that Le Pen's platform of pulling out of the euro would devastate the country's economy and threaten French liberty. The third and forth candidates, Francois Fillon and Jean-Luc Mélenchon were not far behind with 19.94 and 19.64 percent of the votes.
Opinion pollsters predicted Macron to comfortably defeat her by at least 60 percent. It is largely symbolic, as she will only temporarily be replaced by the party's vice president, Jean-François Jalkh, for two weeks, allowing her to concentrate exclusively on the presidential campaign.
She told voters she planned to keep her distance from him, and said being his daughter is "difficult".
During Le Pen's unannounced visit to the factory, where she had been met with enthusiasm, she accused Macron of protecting the interests of oligarchs.
A New York Times story of the French election describes a country where establishment candidates were expected to make it to the runoff in a 11-person election - but obviously failed.
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