Llanelli veteran Jones, who made his Test debut in Wales' record 96-13 defeat by the Springboks in 1998, has been preferred ahead of James Hook.
The rivals have been locked in a ferocious battle for the number 10 jersey and head coach Warren Gatland admitted it was another tight call, with Hook named on the bench.
Gatland said: "We are lucky to have two players of the calibre of Stephen Jones and James Hook competing for the same position.
"I'm very comfortable with the balance of our backline heading into this game."
Llanelli's Dafydd Jones has been named at openside flanker and will win his 13th cap when he runs out at Vodacom Park.
Wales have travelled to South Africa without a specialist number seven and were expected to experiment by playing Jonathan Thomas out of position.
But Thomas has been retained on the blindside with skipper Ryan Jones continuing at number eight and Gareth Delve settling for a place on the bench.
Gatland said: "I have named Dafydd Jones at openside and this is a great opportunity for him to deliver for Wales again.
"With Jonathan Thomas at number six we have two flankers with pace and genuine footballing skills."
Cardiff's Jamie Roberts will win his second cap on Saturday, replacing knee-injury victim Lee Byrne at full-back.
An experienced midfield sees Tom Shanklin and Sonny Parker line-up with Stephen Jones, who partners Gareth Cooper of Gloucester at half-back.
Gatland has retained the core of his Grand Slam-winning tight five of Gethin Jenkins, Mathew Rees, Adam Jones, Ian Gough and Alun Wyn Jones.