Clarke's appointment as test and one-day captain was announced at a news conference today, along with the appointment of allrounder Shane Watson as vice-captain.
Cameron White will continue to captain the Australian Twenty20 team, with Watson as his deputy.
Cricket Australia chairman Jack Clarke said Michael Clarke had proven to be an excellent captain when standing in for Ponting, notably during Australia's recent 6-1 Commonwealth Bank Series win against England.
Clarke, 29, will first lead Australia on its short tour to Bangladesh next month.
"Michael has shown himself to be excellent with his on-field tactics when heading the national side," Jack Clarke said. "To captain your country is a great honour and responsibility and I congratulate Michael and wish him the best in what will be an exciting and challenging time."
Michael Clarke said he was looking forward to the opportunity to lead the Australian team, which he will captain for the first time on next month's short tour to Bangladesh.
"It is a great honour to be appointed captain of Australia, but at the same time, a great surprise as I wasn't expecting Ricky Ponting to stand down," he said.
"I have always respected those who have come before me in this role and humbled to think of my name being mentioned alongside theirs."
Ponting endorsed Clarke as his successor while announcing his retirement.
Watson, 29, said he was looking forward to the added responsibility and working closely with Clarke.
"Playing cricket for Australia has been a great honour for me and to now be appointed vice-captain is really exciting," Watson said. "I look forward to doing what I can to help and support Michael Clarke in the test and ODI teams, and Cameron White with the Twenty20 group.
"There are challenges ahead but also opportunity and I look forward to being part of the leadership group as we work together to grasp that opportunity."
