Nicolas, 71, has run Jesuit operations in east Asia and Oceania since 2004 and spent most of his career in the Far East after being ordained in Tokyo in 1967.
The order said in a statement that Nicolas had been elected to succeed Father Peter-Hans Kolvenbach, who received permission from Pope Benedict to retire as head of the order formally known as the Society of Jesus at the age of 79.
Jesuit superior generals are known as "black popes" because, like the pontiff, they wield worldwide influence and usually keep their position for life -- and because their simple cassock is black, in contrast to the pope who dresses in white.
The 468-year history of the Jesuit order has often included stormy relations with the Vatican. Benedict's predecessor, Pope John Paul, believed the order had become too independent, leftist and political, particularly in Latin America.
Soft-spoken, white-haired Dutchman Kolvenbach won widespread praise for mending relations with the Vatican during his years in the post, after conflicts between his charismatic Basque predecessor and Pope John Paul.
Kolvenbach also had to deal with declining vocations and the future of the order founded by St Ignatius Loyola in 1540.
In the 1960s, the all-male order peaked with some 36,000 members worldwide. It now has about 19,200 members involved in education, refugee help and other social services.
The general congregation that elected Nicolas gathered 217 electors from all over the world at Jesuit headquarters, a block from the Vatican.
They spent four days in prayer and what is known in Latin as "murmuratio," or murmurings, about who should be elected. It is strictly forbidden to lobby for the post and anyone actively seeking the job must be 'turned in' by the other delegates.
The election is by secret ballot and delegates are not allowed to leave the room until Pope Benedict is informed who has won, in keeping with a tradition that the "white pope" is first to know who is the new "black pope."
But unlike a conclave to elect the pontiff, a Jesuit general congregation can continue for weeks or even months after the election to discuss future challenges and priorities.