Clarke tweaked his left hamstring during Australia's first training session on Friday, but jogged several laps on Saturday to lend hope that he may recover in time.
But coach Darren Lehmann said he was not fit enough to take part in Monday's game.
"Michael had a fitness test at training and unfortunately hasn't come through that well enough to be available for selection in game one," he said in a statement.
"He will continue intensive treatment on his hamstring and we'll monitor his progress ahead of game two on Wednesday."
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