The May 7 runoff will pit the centrist independent against the far-right populist.
Exit polls showed Macron, former economy minister, earned the most votes of the presidential candidates, with Le Pen coming in second. Sunday night's results capped a tense day at the polls.
Many of the 67,000 polling stations, which opened early on Sunday, featured a heightened security presence. Last week, a French terrorist with ties to the Islamic State shot and killed a police officer in Paris.
Some pundits predicted a depressed voter turnout as a result of anxiety about terrorism and a dissatisfaction with the candidates. By the end of the day, estimated turnout was at 77 percent, 3 points lower than 2012.
Both the Le Pen and Macron entered Election Day as the front-runners. However, the race had tightened in recent weeks as former Prime Minister Francois Fillon, a conservative, and far-left candidate Jean-Luc Mélenchon generated enthusiasm among dissatisfied French voters.