Jones will be based at the airline's corporate headquarters in Geneva, Switzerland.
In a message to staff today, Air New Zealand's chief executive Christopher Luxon said Jones would leave a big gap at the airline.,
"While disappointed to lose Stephen from Air New Zealand, I am thrilled he has secured this next career step. He beat strong global competition for the position and his success is recognition of both his abilities and the high regard with which our airline is held globally," said Luxon.
Jones had a variety of senior roles, including running domestic, Tasman and Pacific airlines, responsibility for former low cost subsidiary Freedom Air and as manager of investor relations following the recapitalisation of Air New Zealand.
Jones had served as chairman of the Star Alliance management board and the Star Alliance strategy committee.
A replacement was expected to be announced next month and Jones would leave some time before the end of the year when a transition plan was confirmed.