Hayden has been struggling for form in the past few months and Australia's chairman of selectors, Trevor Hohns, said in a statement that he was being given a rest to freshen up.
"The selectors believe that this short lay-off should help Matthew as he prepares for the remainder of the series and all other cricket that lies ahead," Hohns said.
"The 14-man squad will give us the flexibility to give players who have taken part in both forms of the game over the past few months a break from time to time."
Australia play West Indies in Melbourne on Friday in the opening match of the series before playing Pakistan in Hobart two days later.
