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Melbourne: Lee, who will continue to train in South Africa with his Indian Premier League franchise to further his rehabilitation from ankle and foot operations, was included in the 14-man Australian squad last week subject to fitness. In place of speedstar Doug Bollinger join squad.
Selectors decided on Wednesday he would not be capable of bowling full pace in the matches at Dubai and Abu Dhabi.
"The National Selection Panel has been advised by Cricket Australia medical staff that Brett Lee is not yet fit enough to resume international cricket," selection chairman Andrew Hilditch said in a statement. "While it's disappointing for Brett to miss the start of the Pakistan Series, the panel wants to take a careful approach to his return to the Australian team."
"Brett will remain in South Africa to continue the rehabilitation program and gradually increase his bowling volume and intensity," Kountouris said. "I will be monitoring Brett's progress to assess his availability for any part of the series against Pakistan."
Australia won the Test series in South Africa, but is behind 3-1 in the five-match limited-overs series with a match remaining.
The squad for the Pakistan series will assemble on Saturday in South Africa and the series starts April 22.
Lee will train with the Kings XI Punjab squad at Port Elizabeth ahead of the IPL Twenty20 tournament, which was switched to South Africa because of security concerns in India, but is expected to rejoin the Australian squad during the Pakistan series if he's fit enough to resume playing.
Ponting told reporters in South Africa that Lee's outdoor bowling sessions had been interrupted by wet weather in Sydney in recent weeks.
