"I take responsibility for the consequences of this vote and will in the coming days tender my resignation to the boards of Air France and Air France-KLM", Mr Janaillac told a news conference.
The chief government of Air France-KLM raised the stakes earlier within the day, warning he would stop if staff rejected the corporate's newest supply on wages after weeks of rolling strikes by pilots and different employees.
"Competition from Gulf carriers is so fierce that it is really hampering our profitability level", said Jean-Michel Mathieu, CEO of Joon, at an investor meeting in May.
"I hope that my departure will spark a more acute collective awareness", he added.
Janaillac was named chief executive in 2016 with a mandate to ease tensions after years of strikes and labour disputes - including a notorious 2015 incident when two executives had their shirts torn off while escaping workers protesting plans to cut almost 3,000 jobs.
He will officially resign next Wednesday, Air France-KLM said.
Strikes in recent weeks were responsible for huge additional in losses, the company said, with further industrial action planned for May 7 and May 8.
He had been trying to cut costs at the company, amid rising competition from low-priced airlines and Gulf national carriers.
Labour reforms launched by French President Emmanuel Macron have also led to strikes by employees of the state-owned SNCF rail company.
"That has been proved in the cases of the turnarounds achieved by Iberia and British Airways".
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