The 24-year-old won the event, his first serious test since surgery in May last year, at the Victorian Open swimming championships in a time of 49.35 seconds.
Magnussen, who has a personal best in the 100m freestyle of 47.10, missed last year's world championships in Kazan, Russia, where his title went to China's Ning Zetao who won in 47.84.
The Australian is eager to reassert his authority in the pool at the Rio Olympics next August after being pipped for gold at the 2012 London Games by American Nathan Adrian, who won in a time of 47.52.
Magnussen underwent surgery on his troublesome left shoulder after losing 70 percent of his strength in it.
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He lost his 100m national title last year to team mate Cameron McEvoy, who was pipped for the world title by Ning, the first Asian swimmer to win the blue riband event.
McEvoy posted a 48.01 at the Queensland championships in December.
(Reporting by Alan Baldwin in London; Editing by Alison Williams)
