"Michael was assessed by a surgeon in Melbourne early this evening and will be undergoing surgery tomorrow," Australia team doctor Peter Brukner said in a statement.
"Whilst surgery is not always required with hamstring injuries, Michael has substantial damage to a key part of the hamstring tendon and it was felt the best course of action was to surgically repair the damaged area," said Brukner.
"His recovery and the timing of his return to play will be dependent on the surgeon's advice and how well he recovers in the coming weeks," he added.
But, a rejig in the schedule, which led to Adelaide hosting the first Test from December 9, after Philip Hughes' tragic death allowed Clarke to take the field but his chronic back and hamstring problems resurface again in that match which Australia won by 48 runs.
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Clarke has already been ruled out of the three remaining Tests of the ongoing series against India, raising serious doubts over his participation in the World Cup to be co-hosted by Australia and New Zealand in February-March next year.
"There's certainly a chance I could never play again," Clarke had said after the match.
"I hope that's not the case and I'll be doing everything in my power to get back out on the park but I think I've got to be realistic as well.
"I have to be honest with myself and have a long hard think about things, definitely," said Clarke.
In another announcement today, Steven Smith was chosen to captain Australia in the remainder of the Test series against India.