Hughes,25, died Thursday two days after being hit by a bouncer during a domestic game.
"I asked Cricket Australia if Hughesy’s Australian one-day international shirt number, 64, could be retired, to which they agreed. It means so much," Clarke said in a statement.
"Our promise to the Hughes family is that we will do everything we can to honour his memory. He epitomised what the baggy green is about and what it means to us all. Our dressing room will never be the same."
No decision has been announced about the first Test with India, which is due to begin in Brisbane Thursday.