"I accept the consequences of this vote and will tender my resignation to the boards of Air France and Air France-KLM in coming days," said Janaillac after 55.44 percent of Air France workers voted against accepting a pay rise of seven percent over four years.
Unions said the increase was too little after years of restructuring during which pay was frozen, and demanded a 5.1 percent raise this year instead.
Staff and management at the carrier have been locked in a dispute over pay since February.
Janaillac, who had staked his future at the company on winning the vote, deplored Friday's decision as a "huge waste".
"Air France was on the road to success. I regret that that dynamic was not understood (by staff)," he said.
The vote came as workers began a 13th day of intermittent strikes Friday, prompting the cancellation of a quarter of flights on average.
The move coincided with Air France-KLM's release of first-quarter earnings, which showed a net loss of 269 million euros ($322 million), weighed down by three days of strikes during the period which cost about 25 million euros per day according to the company.
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