After defeat in the first Test in Durban last weekend, head coach Stuart Lancaster has revamped his backs by recalling Toby Flood in an attempt to level the three-match series.
Flood's inclusion at number 10 is one of three personnel changes for the clash at Coca-Cola Park with centre Jonathan Joseph being handed his first start and wing David Strettle returning.
Joseph comes in at outside centre with Manu Tuilagi moving inside to take over from the injured Brad Barritt.
Strettle plays on the left wing with Ben Foden reverting to his preferred position of full-back following the loss of Mike Brown for the rest of the series with a thumb injury.
Farrell, who was unconvincing in Durban despite kicking four penalties, must make do with a place on the bench.
Saracens full-back Alex Goode, who was withdrawn at half-time in the midweek match against the Southern Barbarians, is also handed a place among the replacements.
There are no changes in the forwards but prop Alex Corbisiero, fit again after biceps and knee problems, is a replacement.
The decision to axe Farrell, Lancaster's only unforced changed, is the most eye-catching after the 20-year-old excelled in the Six Nations earlier this year. Yet while England showed spirit and endeavour in their narrow 22-17 first Test loss, it was felt the team lacked spark.
Flood, who missed the end of the domestic season through injury, brought added impetus from the bench and he will now have the chance to do that from the start.
The 26-year-old will win his 49th cap and be reunited with his Leicester team-mate Ben Youngs in the halves.
Lancaster said: "Owen has had a fantastic season and I am sure he will make a significant impact from the bench.
“However, Toby has waited patiently for his opportunity and the time is right to allow him the chance to demonstrate his experience and skills in what will be a very tough challenge."
England: B Foden; C Ashton, J Joseph, M Tuilagi, D Strettle; T Flood, B Youngs; J Marler, D Hartley, D Cole, M Botha, G Parling, T Johnson, C Robshaw (captain), B Morgan. Replacements: L Mears, A Corbisiero, T Palmer, P Dowson, L Dickson, O Farrell, A Goode.
South Africa: P Lambie; J P Pietersen, J de Villiers (capt), F Steyn, B Habana; M Steyn, D Hougaard; T Mtawarira, B du Plessis, J du Plessis, E Etzebeth, J Kruger, M Coetzee, W Alberts, P Spies. Replacements : A Strauss, W Kruger, F van der Merwe, K Daniel, R Pienaar, B Basson, W Olivier.