The Kiwi confirmed on Thursday he would extend his contract beyond the British and Irish Lions tour, but won't continue through to the showpiece tournament on home soil.
His last Test in charge will be against the All Blacks in Perth on October 4.
The departure of the 59-year-old forces the governing body to search for a fifth Wallabies coach in six years.
Queensland's Les Kiss, Waratahs mentor Dan McKellar and the Brumbies' Stephen Larkham are understood to be in the running although RA is set to explore all options.
Former Wallabies boss Michael Cheika, who was at the helm for 68 Tests between 2014 and 2019, is another option after recently announcing he would step down as coach of UK club Leicester Tigers at the end of the current season.
The new coach will steer the Australians on the spring tour, with their first clash on October 25 in Tokyo against Japan, now looked after by Eddie Jones, who was Wallabies mentor before Schmidt.
Australia's 2024 Spring tour included wins over England and Wales and a narrow loss to Ireland, which increased optimism over the direction of the Wallabies after the disastrous World Cup under Jones in France.
However Schmidt's wife and son, who requires constant medical care, live in New Zealand which swayed his decision.
It's believed Schmidt is open to staying on as a consultant but that would be dependent on the new coach although he gave nothing away in a brief statement.
"I am very much enjoying my time with Australian rugby," Schmidt said.
"The British and Irish Lions is our immediate focus but, with the Rugby Championship following so closely after the Lions series, I understand the need for continuity heading into two away Test matches against South Africa."
RA director of high performance Peter Horne said they were happy Schmidt was on board for the Rugby Championship given it starts two weeks after the third and final Lions Test in Sydney on August 2.
The Australian team will fly to South Africa to take on the world champions in back to back Tests on August 16 and 23.
They will then play Argentina in two matches in Australia before taking on New Zealand at Eden Park in Auckland and in Perth, with those games doubling as Bledisloe Cup fixtures.
"We are delighted Joe will continue to coach the Wallabies beyond his current contract," Horne said in the statement.Â
"After noting the positive impact Joe has made with the Wallabies' playing and coaching staff, we were keen that he stay on after the Lions series."Joe expressed to us that he was enjoying his work with the Wallabies while also making clear his need to spend more time at home with his family."
RA boss Phil Waugh thanked Schmidt for his help in "restoring pride in the Wallabies jersey".
"Joe's drive, knowledge and work ethic have been instrumental in restoring pride in the Wallabies jersey and energising supporters around the country," Waugh said.
"We are pleased that Joe has extended his involvement with the Wallabies beyond his initial contract and look forward to beginning the process of recruiting his successor."
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