Young fast bowlers Patrick Cummins and James Pattinson were selected for both squads, while rising all-rounder Mitchell Marsh claimed a berth in the T20 lineup.
'South Africa will be an extremely tough tour. South Africa is a very strong side and playing them away is always difficult,' said chairman of selectors Andrew Hilditch.
'It will be another great test for the Australian side but we are confident they are up for the challenge.'
He said Johnson missed out of the T20 squad after inconsistent performances, although he made the one-day line-up.
'Mitchell has struggled in this format of the game to date. Most Twenty20 internationals have been at the start of tours and Mitchell has not always been at his best in these matches,' said Hilditch.
'His place has gone to Doug Bollinger, who is very experienced in this form of the game and his consistent performances in Twenty20 cricket have led to him forcing his way into the side.'
The one-day squad sees two changes to the one that recently beat Sri Lanka 3-2, with Hussey dropped and David Warner taking his place. John Hastings is injured with Patrick Cummins filling in for him.
'We did not think that David (Hussey) quite took his opportunity in Sri Lanka and his place has been taken by David Warner,' said Hilditch.
'David's form has been irresistible recently and he deserves this opportunity in the one day squad.'
The Test squad will be announced next month.
T20: Cameron White (capt), Shane Watson, Doug Bollinger, Patrick Cummins, Aaron Finch, David Hussey, Brett Lee, Mitchell Marsh, Shaun Marsh, Stephen O'Keefe, James Pattinson, Steven Smith, Matthew Wade, David Warner.
ODI: Michael Clarke (capt), Shane Watson, Doug Bollinger, Patrick Cummins, Xavier Doherty, Brad Haddin, Mike Hussey, Mitchell Johnson, Brett Lee, Shaun Marsh, James Pattinson, Ricky Ponting, Steven Smith, David Warner.