Hughes died on Thursday aged 25 two days after being hit by a ball.
Clarke said: "I asked Cricket Australia if Hughesy's one-day international number 64 could be retired, to which they agreed. That means so much."
Hughes's funeral will be on Wednesday and Australia's first Test against India will not start on Thursday. Pausing frequently to wipe away tears, Clarke said: "Our promise to Hughesy's family is that we will do everything we can to honour his memory. "He epitomised what the baggy green is all about and what it means to us all.
"Our dressing room will never be the same. We loved him, and always will. Rest in peace." Before its delayed start was announced, former Australia captain Ricky Ponting said the Test match against India in Brisbane should not start on Thursday.
"I don't think it would be right," he said. "Even if the boys think they can play it would be a miracle if they find the right frame of mind needed for five days of cricket."