Australia's leading batsman, Clarke flew home from Zimbabwe recently after aggravating his left hamstring injury during a one-day international tournament.
"Since returning to Australia Michael has had a series of investigations that have confirmed a significant hamstring injury," Cricket Australia physiotherapist Alex Kountouris said in an Australian Cricket Board statement on Tuesday.
"Importantly, the scans have demonstrated tendon damage which complicates the recovery from this injury.
"As such, he will not recover in time to be available for the ODI series in the UAE."
Australia's selectors had named Clarke captain of the 15-man squad for the Tests and skipper of the 14-member ODI squad released last week.
After a one-off Twenty20 match on Oct. 5, Australia play Pakistan in the three one-dayers before the first Test starts Oct. 22 in Dubai.
"We are hopeful that he will be available for the Test series but this will be determined at a date closer to the first Test," Kountouris added.