Hayden averaged 19.50 during the series defeat against South Africa
Matthew Hayden has been left out of Australia's one-day international and Twenty20 squads to face South Africa.
The 37-year-old opener has been out of form lately and his exclusion increases speculation over his Test future.
Exciting young opener David Warner gets his chance in the Twenty20 version of the game, while paceman Shaun Tait has been named in both squads.
Australia host the Proteas in Twenty20 games on 11 and 13 January before the one-day series begins on 16 January.
All-rounders Andrew Symonds (knee) and Shane Watson (back) are unavailable due to injury, while Michael Clarke will sit out the Twenty20 games because of a thumb problem.
National selection panel chairman Andrew Hilditch said the squads were chosen with this year's ICC World Twenty20 and the 2011 World Cup in mind.
The omission of Matthew Hayden is not a reflection on his performances in the recent Test series
He said the absence of Hayden, a veteran of 103 Tests who averaged just 19.50 during the recent three-match Test series against South Africa, was because Australia were planning for the future.
Hilditch said Hayden's omission "is not a reflection on his performances in the recent Test series but rather a strategic decision made by the national selection panel as we plan for these signature events".
"His possible selection for the upcoming tour of South Africa will be discussed, as with all players, when we select a squad after the round of interstate matches at the beginning of February," added Hilditch.
"Winning a fourth consecutive ICC World Cup and our first ICC Twenty20 title is an ambitious project.
"For this reason there will be very few players selected from this point that we can not see playing a role in achieving this goal."
Mitchell Johnson will be rested from the Twenty20 matches and the first two one-day games after his heavy workload during the 2-1 series defeat to the Proteas.
Clarke, who sustained ligament damage to his right thumb during the first Test against South Africa in Perth, is unavailable for the Twenty20 clashes in Melbourne and then Brisbane two days later.
Team physiotherapist Alex Kountouris said he was hopeful Clarke would be available for the first one-dayer at the MCG.
"This injury has required pain killing injections in every batting innings since and for this reason we have decided the best course of action is for him to miss the first two Twenty20 matches," said Kountouris.
"We will continue to monitor the injury over the next four to five days and we are very hopeful of him being fully fit for the beginning of the Commonwealth Bank Series."
Australia Twenty20 squad: Ricky Ponting (capt), Michael Hussey (vc), David Hussey, Ben Hilfenhaus, James Hopes, Nathan Bracken, Brad Haddin, Shaun Marsh, Shaun Tait, David Warner, Ryan Harris, Cameron White, Nathan Hauritz.
Australia one-day international squad: Ricky Ponting (capt), Michael Clarke (vc), Brad Haddin, James Hopes, Nathan Bracken, Shaun Marsh, Michael Hussey, David Hussey, Nathan Hauritz, Ben Hilfenhaus, Cameron White, Shaun Tait, Peter Siddle.