Clarke, who did not play in Australia's first two Group A matches in the tournament, will return home for treatment though it is not immediately known for how long he will be out of cricket.
"Michael has had lower back pain since the latter part of the one-day series in England. On arriving in South Africa the pain has intensified and he has not been able to participate in any of the team's training sessions," Cricket Australia physiotherapist Alex Kountouris said in a statement.
"He has received intensive treatment but it is apparent that he will not be able to take any part in the remainder of this series. Michael will return home to continue his treatment and return to playing as soon as possible," Kountouris added.
CA said a decision on a replacement player will be made by the National Selection Panel in due course for confirmation by the ICC as per Champions Trophy protocol.
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