Clarke was left out of the squad for the Commonwealth Bank Series games on January 11 and 13.
The retiring Michael Hussey has also been left out of the 13-man squad, along with David Warner, Matthew Wade, Dan Christian and James Pattinson.
National Selector John Inverarity said: "Michael (Clarke) has been battling a hamstring injury for a few weeks and will have a break, as will Matthew Wade and David Warner. These three players have played in all six Vodafone Test matches this summer and the intention is to have them returning to the ODI squad refreshed.
"Taking a long term view towards the ICC Cricket World Cup the NSP has decided not to include Michael Hussey in the squad for the Commonwealth Bank Series. Michael has been a tremendous ODI player for Australia over a long period of time, a match-winner for his country and his presence in coloured clothing will be sorely missed.
"James Pattinson, together with Shane Watson, were not considered for selection in these two games as they are yet to return to full fitness, while Dan Christian has not been included in the squad.
"The squad has a number of young players who have a considerable upside. The seven batsmen have all performed very well when their last 10 appearances in 50 over cricket are considered."
George Bailey will captain Australia in the first two matches.
The Australian squad for the first two matches:
George Bailey (captain), Ben Cutting, Xavier Doherty, Aaron Finch, Brad Haddin, Phillip Hughes, David Hussey, Mitchell Johnson, Usman Khawaja, Glenn Maxwell, Clint McKay, Steve Smith, Mitchell Starc.