While Clarke will sit out the match, spinner Nathan Lyon will return to the side for the first time in over two years.
"Michael had a fitness test at training today and unfortunately hasn't come through that well enough to be available for selection in game one,” coach Darren Lehmann said in a statement released by Cricket Australia.
“He will continue intensive treatment on his hamstring and we'll monitor his progress ahead of game two on Wednesday.”
The side will now be lead by George Bailey and will include a return for Lyon, who has not played for the 50-over side since March 2012.
"Looking at the wicket today, we've opted to go with the spin option of Nathan Lyon along with the extra all-rounder to add further depth to our batting line-up which means that Phil Hughes has unfortunately missed out on selection," Lehmann said.
Australia: George Bailey (captain), Aaron Finch, James Faulkner, Brad Haddin, Mitchell Johnson, Nathan Lyon, Mitchell Marsh, Glenn Maxwell, Kane Richardson, Steve Smith, Mitchell Starc
(Reporting by Nick Said, editing by Pritha Sarkar)
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