The right-arm quick, who missed Australia's domestic Twenty20 competition in January, returned to the international field in the second test against New Zealand in Christchurch where he impressed with his pace and bristling aggression.
The 25-year-old took six wickets in the match at Hagley Oval, including 4-77 in New Zealand's second innings that helped reduce the target Australia needed to chase to seal the seven-wicket victory.
"James had a recurrence of his left shin soreness following the second test in Christchurch and had follow-up scans in Melbourne yesterday," Cricket Australia physiotherapist David Beakley said in a statement on Tuesday.
"These scans have shown some inflammation around the shin consistent with bone stress.
"James will now require some time off to allow this injury to resolve and will not be available for the remainder of the domestic cricket season."
Pattinson was not in Australia's squad for their short limited overs tour of South Africa before the World Twenty20 in India, which begins next week.
(Reporting by Greg Stutchbury in Wellington; Editing by Patrick Johnston)
