Ponting will return to Britain to take charge for the bulk of one-day international series but the selectors wanted to give him a rest as they start blooding younger players for next year's Twenty20 World Cup in West Indies.
"Ricky Ponting is having his workload managed and will return home to Australia after the fifth test at The Oval and will miss the ODI against Scotland, the two Twenty20s and the start of the of the ODI series against England," Australia's chairman of selectors Andrew Hilditch said in a statement on Tuesday.
"This is the last opportunity we have to give Ricky a break until next year, with the ICC Champions Trophy, ODIs against India and of course a full domestic summer against the West Indies and Pakistan to finish 2009.
"The plan for him to return to Australia before rejoining the team is considered the most appropriate course of action.
"This gives Michael Clarke another opportunity to captain the Australian Twenty20 and ODI side."
Clarke's promotion is a further sign that he is being groomed to eventually replace Ponting as test skipper.
Clarke is the current vice-captain of the test side and has been Australia's best batsmen this year, scoring two hundreds and averaging 89 in the Ashes.
The selectors named separate squads for the Twenty20 matches and one-day internationals as part of their building process for the West Indies next year.
Promising opener Phillip Hughes and paceman Stuart Clark failed to make either side while batsman Mike Hussey and pace bowlers Peter Siddle and Nathan Bracken made the one-day side but not the Twenty20.
"We obviously know what Mike Hussey and Nathan Bracken are capable of in one-day and Twenty20 cricket, but with limited opportunities at international level in this format of the game we wanted to look at different players as we look to improve our Twenty20 performances," Hilditch said.
"Their omissions do not mean we won't look to them for the World Twenty20."
