The man known as "the missile" clocked 47.71 seconds, with Jimmy Feigen of the United States taking silver in 47.82 and his compatriot Nathan Adrian, the Olympic champion, bronze in 47.84.
The only men to have previously won two straight 100 freestyle world titles are American Matt Biondi, Alexander Popov of Russia and Italian Filippo Magnini.
Adrian pipped Magnussen into second place by one hundredth of a second to win Olympic gold in London last year.
(Reporting by Iain Rogers; Editing by John Mehaffey)
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