Cheika had come under fire in the Australian media for keeping faith with the so-called "Pooper" combination because of the negative impact playing the two openside flankers had on the Wallabies lineout.
His solution was to bring lineout jumper Dean Mumm, who usually plays at lock, into the back row for Fardy, who has all but owned the Australia number six shirt for the last four years.
In the other personnel change to the starting line-up for Saturday's Lang Park test, Reece Hodge will win his second cap on the left wing with Dane Haylett-Petty switching to right flank in place of the injured Adam Ashley-Cooper.
The Wallabies lost their opening two tests in the Rugby Championship to world champions New Zealand and will be desperate for a victory over the Springboks to end a run of six defeats going back to last year's World Cup final.
Cheika has also retained Quade Cooper at flyhalf with Bernard Foley outside him in the inside centre position, a combination that had limited success in the loss to the All Blacks in Wellington two weeks ago.
Hulking Tongan-born Lopeti Timani, who can play at lock or number eight, could win his first cap off the bench in the match and follow in the footsteps of his brother Sitaleki.
Rory Arnold, another second row option, was also named on a nine-man bench after recovering from an elbow injury that kept him out of the first two tests.
Hodge came off the bench to make his test debut in the Wellington test and was preferred on the wing to Drew Mitchell, who is on the bench after coming through a fitness test on a groin injury that has kept him out of action since May.
One player will be omitted from the named replacements, most likely on Saturday.
Team: 15-Israel Folau, 14-Dane Haylett-Petty, 13-Samu Kerevi, 12-Bernard Foley, 11-Reece Hodge, 10-Quade Cooper, 9-Will Genia, 8-David Pocock, 7-Michael Hooper, 6-Dean Mumm, 5-Adam Coleman, 4-Kane Douglas, 3-Sekope Kepu, 2-Stephen Moore (captain), 1-Scott Sio.
Replacements (one to be omitted): Tatafu Polota-Nau, James Slipper, Allan Ala'alatoa, Rory Arnold, Lopeti Timani, Sean McMahon, Nick Phipps, Tevita Kuridrani, Drew Mitchell.
(Reporting by Nick Mulvenney; Editing by Ian Ransom)
