Australia, ranked second in the world in one day internationals, will play seven ODIs and one Twenty20 against India, who are ranked number one in the 50-over format.
"Michael Clarke's back condition has flared up again and he has been selected subject to fitness," selector John Inverarity said in a statement.
"He has returned to Australia for further assessment and the(we) hope that it will improve in time for the Indian tour."
Clarke was, however, hopeful that his recurring back problem would heal in time for him to make the tour.
"No doubt it's quite stiff and sore," Clarke told reporters on his arrival back in Australia on Wednesday.
"But I'll be guided by the experts on what I need to do now to try and get myself as fit as I can be."
Matthew Wade was dropped to make way for Haddin after scoring just 36 runs at an average of 12 in the just completed five-match ODI series against England, which Australia won 2-1.
"Matthew Wade has been omitted due to lack of form and has been replaced by Brad Haddin, who captured an Ashes series record of dismissals in July and August," Inverarity added.
All-rounder Moises Henriques came in for the injured top-order batsman Shaun Marsh, who suffered a hamstring injury during the fourth ODI against England.
There was also no place for legspinner Fawad Ahmed, who made his debut against England earlier this month but took just two wickets at a cost of 106 runs in two matches.
Left-arm tweaker Xavier Doherty was preferred
"Xavier Doherty has been included in the squad in place of Fawad Ahmed as (we) feel that he is well suited to ODIs in India," Inverarity added.
"Fawad bowled well with his limited opportunities in the rain affected series and better than his figures would suggest."
Fielding coach Steve Rixon will take the charge of the team in place of regular head coach Darren Lehmann, who has been rested for the tour.
"Darren has been on the road and away from home for a considerable amount of time," general manager Pat Howard said. "This is a great opportunity for Darren to refresh, work with the states and provide others with opportunities."
Squad: Michael Clarke (captain), George Bailey, Nathan Coulter-Nile, Xavier Doherty, James Faulkner, Aaron Finch, Brad Haddin, Moises Henriques, Phil Hughes, Mitchell Johnson, Glenn Maxwell, Clint McKay, Adam Voges, Shane Watson.
- Sports & Recreation
- John Inverarity
- Brad Haddin
- Matthew Wade
- Moises Henriques