The 33-year-old batsman suffered the problem in the first ODI against South Africa earlier this month. Pace bowler Ryan Harris is also included for the first time since March after knee surgery.
The third instance of Clarke injuring his left hamstring in the space of six weeks caused him to miss the remaining four ODIs against South Africa in a series that Australia won 4-1, The BBC reported.
Clarke, who has scored 8,297 runs in 107 Tests, will play for a Cricket Australia XI against the tourists in a two-day match beginning on 28 November if he continues to respond to daily treatment.
Ten of the 12-man squad played in every match of Australia's 5-0 Ashes whitewash last winter, with batsman Mitchell Marsh and uncapped seamer Josh Hazlewood also included.
Meanwhile, India would be led by batsman Virat Kohli at the Gabba in the absence of regular captain Mahendra Singh Dhoni. The first of four Tests begins in Brisbane on 4 December.
The Australia squad is: Michael Clarke (captain), Chris Rogers, David Warner, Mitchell Marsh, Steve Smith, Shane Watson, Brad Haddin, Nathan Lyon, Josh Hazlewood, Mitchell Johnson, Peter Siddle, Ryan Harris.