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Stoinis had injured his right shoulder during a training session with his Indian Premier League (IPL) franchise Kings XI Punjab earlier this month, making him a doubtful starter for the International Cricket Council (ICC) event.
After initial scans in India, Stoinis had returned to Australia to rehabilitate.
A Cricket Australia spokesperson (CA) confirmed the 27-year-old Stoinis had passed his fitness test, saying on the CA site that "he bowled today and medical staff were happy with his progress".
Stoinis played five matches in the IPL, scoring only 17 runs in three innings and taking two wickets before being ruled out.
He has played three One-day Internationals (ODI) for Australia and has a batting average of 96 in the format, primarily courtesy his unbeaten 146 against New Zealand in January.
Australia will start their Champions Trophy campaign against New Zealand in Birmingham on June 2.
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