"Pat returned home early from the Australia A tour of Africa with some side/back soreness and scans have shown a partial recurrence of his lower back bone stress injury suffered in October last year," CA Chief Medical Officer Justin Paoloni said.
"He will be closely monitored to determine his return to the playing field, but expect that he will miss most of the 2013-14 domestic cricket season."
In June, Pattinson toured England with the A team after being sidelined for nine months with a back injury but did not play a match.
Australia have been heavily protective of the fast bowler and opted against rushing him back. The latest injury means he will also miss the home Ashes series against England starting in November.
Australia, who trail England 3-0 ahead of the final test of the current Ashes series starting on Wednesday at The Oval in London, lost another young fast bowler, James Pattinson, to injury during the series.
Pattinson complained of hip and back soreness during the second test at Lord's and was subsequently ruled out of the remainder of the five-match series.
(Reporting by Sudipto Ganguly in Mumbai; editing by Patrick Johnston)
