The matches will be played Jan 11 at the Melbourne Cricket Ground and Jan 13 at the Adelaide Oval in Adelaide.
Other names missing from the last Australian ODI team that played Pakistan in Sharjah Sep 3 are David Warner, Matthew Wade, Dan Christian and James Pattinson.
"Michael 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 Test matches this summer and the intention is to have them returning to the ODI squad refreshed," said national selector John Inverarity.
"Taking a long term view towards the ICC Cricket World Cup, the NSP has decided not to include Mike Hussey in the squad. Mike 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 as they are yet to return to full fitness, while Dan Christian has not been included in the squad," added Inverarity.
The squad announced has many young players who have performed well in their last 10 appearances in 50 overs cricket.
George Bailey will be the captain in the absence of Clarke. In addition, Dean Jones has been named as batting coach.
The Australian squad for the first two matches: George Bailey (C), Ben Cutting, Xavier Doherty, Aaron Finch, Brad Haddin, Phillip Hughes, David Hussey, Mitchell Johnson, Usman Khawaja, Glenn Maxwell, Clint McKay, Steve Smith, Mitchell Starc.
