Nicolas Demorand's restructuring plan was denounced by the paper's journalists in a front-page story at the weekend.
He had already suffered four votes of no confidence from its editorial board.
Mr Demorand had led the paper since March 2011.
In an interview with another newspaper, Le Monde, he said he hoped his departure would help "revive the dialogue needed to take the newspaper out of the crisis".
The dispute has caused turmoil at the paper, which was co-founded in 1973 by French philosopher Jean-Paul Sartre.
Under the restructuring plan, the paper would have been turned into a social network, providing content for multimedia platforms.
The paper's headquarters would have become a cultural centre, with a bar, a restaurant, a TV studio and a start-up hub.
Key shareholders defended the plan as the only viable future for the ailing 40-year-old paper, which saw its sales slide 15% last year.
But journalists accused the management of wanting to turn Liberation into a brand and said the plan involved doing everything but journalism.
After staging a one-day strike, the journalists decided to return to work and use the pages of Saturday's edition to attack the plan.
The editor-in-chief of left-leaning French newspaper Liberation has resigned after a bitter row with staff over his plans to transform the paper into a social network.