He was handed the leadership of Australia's 12-man squad for the one-off clash, while Ponting and opener Matthew Hayden take a break ahead of the Chappell-Hadlee one-day series against New Zealand.
Clarke said he was surprised when told the news by chairman of selectors Andrew Hilditch, initially fearing he had been dropped from the side.
"I was thinking (Hilditch) wants to talk to me and it is always bad news, especially over the phone, so I was thinking gee, I hope I'm not going to be dropped," said Clarke.
"I was over the moon, I didn't know what to say.
"I see it as a great opportunity, no doubt. But let's definitely make it clear Ricky Ponting is still the Australian cricket captain."
Clarke is seen as Ponting's long-term replacement but admits he has little experience at the top, with his last time in charge coming three years ago for Australia A.
"I haven't had any recent experience, so it's going to be another challenge for me," Clarke said. "I will definitely speak to Ricky and get his help and advice."
Australia will play New Zealand in the Twenty20 in Perth on Tuesday ahead of a one-day series starting December 14.
Australia: Michael Clarke (capt), Adam Gilchrist, Andrew Symonds, Michael Hussey, Brad Hodge, Adam Voges, Ashley Noffke, Brett Lee, Nathan Bracken, Stuart Clark, Mitchell Johnson, Shaun Tait.