A thorn in the side of President Francois Hollande's Socialist government, the reform-minded minister handed in his resignation after sailing down the Seine River for the meeting at the Elysee Palace with his one-time champion.
The president's office released a statement saying Macron had resigned and that Finance Minister Michel Sapin would take over the economy portfolio.
The former investment banker and self-made millionaire quit "to dedicate himself entirely to his political movement", the presidency said, referring to "En Marche" (On the Move), which he founded in April.
Marine Le Pen, 48, of the far-right anti-immigration National Front, is standing for a second time in elections set for April 23 and May 7, 2017.
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Macron's departure is a blow to Hollande, whose approval ratings are the lowest of any post-war French president. He has pledged not to seek re-election if he fails to rein in stubbornly high unemployment, which is hovering at around 10 percent.
Hollande, who has already alienated the left flank of the Socialist Party through economic and labour reforms, faces further isolation with the loss of the star of his government's centrist side.
Macron launched "En Marche" (On the Move) in April saying he wanted to promote "new ideas ... Neither of the right nor the left".
In a speech last month he left little doubt as to his intentions, pledging to lead the movement "to 2017 and to victory".
Macron, like most French politicians a graduate of the prestigious Ecole Nationale d'Administration, indirectly criticised Hollande by describing France as "a country worn down by broken promises".
A maverick in politics as well as in his private life, Macron is married to a divorcee with three children who is some 20 years his senior.
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