The 42-year-old maestro, who heads the Paris Opera, already waltzed into the Austrian music world three years ago when he took over as chief of the Vienna Symphony Orchestra.
The announcement was made by the opera's new director Bogdan Roscic who will start his role at the same time as Jordan.
"Philippe Jordan is one of the rare important conductors today to have devoted himself to opera from the very start of his artistic career," said Roscic who is currently president of Sony Music's classical music division.
"His knowledge and experience will be of crucial benefit to the opera."
The Vienna Opera has been without an official musical chief since the 2014 resignation of Austrian conductor Franz Welser-Moest.
Jordan, who has been at the helm of the Paris Opera since 2009, is a renowned specialist in the works of composing giants Giuseppe Verdi and Richard Wagner.
He comes from a musical family, with his late father Armin having served as conductor of Switzerland's Orchestre de la Suisse Romande in Geneva from 1985 to 1997.