Clarke revealed Hughes' one-day shirt number would be retired.
"Our promise to Hughesy's family is that we will do everything we can to honour his memory," he said.
Watch: Phillip Hughes 1988 - 2014
"Last night, I asked Cricket Australia if Hughesy's Australian one-day international shirt, number 64, could be retired - to which they agreed."
Clarke added that Hughes' legacy of "trying to improve each and every day will drive us for the rest of our lives".
"We'd like to thank everyone here and overseas for the touching tributes to Hughesy in recent days," he said.
"Our dressing room will never be the same. We loved him and always will. Rest in peace bruzzy."
Clarke's emotional words came as cricketers around Australia started taking the field on a sombre Saturday. Grade cricket in Sydney and Adelaide, the two cities where Hughes plied his trade as a professional cricketer, was cancelled.
But club and school games otherwise largely went ahead as planned, with the cricket community continuing to grieve the shock death of Hughes.
Players - young and old - donned black armbands and stood for 63 seconds of silence at matches around Australia.
Cricket Australia asked that the mandatory retirement score for junior players be lifted from the traditional 50 to 63.
Hughes was unbeaten on 63 batting for South Australia on Tuesday when he played his last stroke.
The left-hander was Australia's 408th test player and the number has been painted on cricket fields around the country.
Tributes continue to flow from around the world, with the Queen sending a private message of condolence to the Hughes family.