Governing body Rugby Australia also announced that Cheika must work with a three-man selection panel -- himself, Johnson and an independent -- in an overhaul to halt the team's alarming slide in form ahead of the World Cup in Japan next year.
Cheika has faced a mounting backlash from dismayed fans and former players after winning just four of Australia's 13 Tests this year -- their worst campaign in decades.
Despite the dire results and a drop to sixth in the world rankings, Rugby Australia chief Raelene Castle has consistently backed him to take the Wallabies to Japan.
His coaching team of Stephen Larkham, Nathan Grey and Simon Raiwalui also survived, for now, despite widespread calls for change.
"We are confident that Michael is the right man to lead the Wallabies to the rugby World Cup and the appointment of Scott Johnson will support Michael and his coaching team as they prepare for the tournament in Japan next September," Castle said Monday.
"Scott Johnson has built a strong reputation in the international rugby landscape over more than a decade, and since taking over as director of rugby in Scotland the national team has climbed to its highest ever world ranking of fifth."
She added that Johnson would take responsibility for the management of the Wallabies' off-field programme, which would allow Cheika "to focus on what he does best, which is coaching the team".
The fate of Cheika -- world coach of the year in 2015 -- has split the rugby world with some, including Wallabies legend Matt Burke, describing his position as "untenable". But others threw their support behind him as the best man for the job.
"It's a great move for Australian rugby and I know it will prove to be the best long-term structure for the game in this country," said Cheika.
"I'm looking forward to working with Scott and finishing the work that I started by making Australians proud of our performance."
Sydney-born Johnson, 56, became Scotland's director of rugby in 2013 and has overseen their recent renaissance. He also served as Scotland's interim coach from 2012-2014.
"I am excited to be returning to Rugby Australia in the director of rugby role and I am looking forward to supporting Michael and the Wallabies in their build-up to the World Cup," said Johnson, who last worked with Australia at the 2007 World Cup as attack coach under John Connolly.
Part of his job, which he will take up in mid-March, will also be to oversee a new National High Performance Plan in concert with the country's four Super Rugby franchises.
No specific details were released but reports last month said part of the plan would be to rest key players during next year's Super Rugby season in a bid to keep them fresh and injury-free for the World Cup.
The move is based on a New Zealand programme that ensures top players are monitored and given time off, including missing Super Rugby games.
"It has been a tough year for all who love rugby, and this is an important step in building a strong, successful and sustainable future for Australian rugby and getting the Wallabies back to where they belong," said Castle.AFP