The Air France-KLM board asked Mr Janaillac to stay on until May 15 when it will put a transitional leadership in place.
The French Minister of Economy and Finance, Bruno Le Mairie, appealed "to reason" to striking Air France workers. He promised a 7% wage increase over four years, but included scope to adjust that level if Air France's annual financial result was less than €200 million and to apply a reversion clause in case of higher inflation or a negative financial result.
The firm's CEO Jean-Marc Janaillac announced his resignation on Friday after staff at the carrier's French operations rejected a pay deal aimed at ending months of walkouts.
Unionised staff walked out for the 14th day on Monday as they press for a 5.1-percent salary increase this year as the company recovers from years of losses and restructuring.
Janaillac warned previous year that volatile fuel prices and geopolitical risks could threaten the company's turnaround, but didn't appear to predict the heavy toll that the strikes would take.
CEO Jean-Marc Janaillac's attempt to cut costs at the carrier to keep up with competition from budget airlines and Gulf rivals ran into strong union resistance, as had his predecessor's efforts, raising questions over its ability to reform.
The Air France passenger website has warned customers that despite presenting an up-to-date flight schedule earlier Monday with 80% of all planned flights still expected to operate, late cancellations due to the strike action could still occur.
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Air France warned that industrial action would continue to affect its services today and tomorrow.
Air France-KLM posted a first quarter operating loss of €118 million ($141 million) last week, attributing €75 million of that loss to the strike impact.
Mr Le Maire told French news channel BFM TV: "I call on everyone to be responsible: crew, ground staff, and pilots who are asking for unjustified pay hikes".
Bloomberg reports that the airline group's stock has dropped as much as 14 percent as of Monday, the biggest decline since 2002.
"If Air France does not become more competitive".
A May 4 electronic vote resulted in a "no" vote to the plan by a majority of Air France staff.