The 33-year-old, who has a catalogue of back and hamstring trouble, was forced to retire hurt in a one-dayer against Zimbabwe in Harare on August 31 and returned home from the tour early.
Scans have since revealed tendon damage in the affected area and he will have to sit out the team's final one-day tour before hosting the World Cup next year, Cricket Australia physiotherapist Alex Kountouris said.
"Since returning to Australia, Michael has had a series of investigations that have confirmed a significant hamstring injury," Kountouris said in a statement.
"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 United Arab Emirates."
"We hope he will be available for the Test series, but this will be determined at a date closer to the first Test."
The three-game one-day series against Pakistan starts on October 7 with the first of two Tests not until October 22.
On his early return to Australia from Zimbabwe, Clarke was adamant that his ongoing hamstring and back problems would not result in a premature end to his one-day career.
"It's hard for me to look any further down the track than where I am today but I love the game as much as I ever have and the last thing I am thinking about is retiring," he said then.
Pakistan have been forced to play their home series at neutral venues, such as the UAE, since militants attacked the Sri Lankan team in Lahore in 2009.
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