Warriors flanker Sanderson, capped nine times, replaces Martin Corry as skipper after England head coach Andy Robinson opted to rest the Leicester number eight.
Robinson plans to announce his 30-man tour squad at Twickenham on Monday, but he has confirmed Corry and a "number of other players" will sit out the trip, which features clashes against Australia in Sydney on June 11 and Melbourne six days later.
Northampton pair Steve Thompson and Ben Cohen have already announced they will not be travelling, while props Andrew Sheridan and Matt Stevens are injured and the likes of Josh Lewsey and Lawrence Dallaglio are also expected to take a breather.
Corry led England in all eight of their Tests this season, but the captaincy role now goes to 28-year-old Worcester skipper Sanderson, who missed the entire Six Nations Championship campaign because of injury.
Sanderson skippered England A to victory in last summer's Churchill Cup, and made his senior debut during the 1998 tour when England suffered comprehensive defeats against Australia, New Zealand (twice) and South Africa.
Moves to rest Corry come as no surprise, especially as he was involved in last summer's punishing British & Irish Lions tour of New Zealand and has been a virtual ever-present during Robinson's 16-Test reign.
"Martin has done an outstanding job as captain of England this season and has led by example, but along with a number of other players, I think it is important Martin is rested for the summer tour," said Robinson.
"He has had a long season, preceded by the Lions tour, and it is crucial that he has a summer off and then prepares for his club and country commitments in 2006/07, leading up to and including the Rugby World Cup in 2007.
"Pat Sanderson has accepted the role of captain for the Australia tour, and like Martin he has the qualities I am looking for in that role.
"He has led Worcester Warriors well, and has made a complete return to form from the injury he sustained earlier in the season. I am sure he will do an excellent job for the side."
Corry admitted he would like to travel with England down under, but rest would be crucial this summer as he prepares for next season's considerable challenges.
Corry said: "Andy and I had a good meeting this week, and while I would like to go on the tour, I also have to listen to his advice and what my body is telling me to do and have some rest before preparing for what will be an exciting and challenging season next year."
Sanderson, who made his Test debut against the All Blacks in Dunedin almost eight years ago, will lead a squad which is likely to include young guns such as Leicester wing Tom Varndell, Newcastle centre Mathew Tait and Sale Sharks flanker Magnus Lund.
"Martin led England well last autumn when I was playing with him in the back row, and my aim now is to take his own high standards with me to Australia," said Sanderson.
"I was privileged to lead England in winning the Churchill Cup last summer, and this is another huge honour for me and my family.
"I will do everything I can to help England perform well against the Wallabies."