The Newcastle fly-half takes over from Jason Robinson, who has not recovered from a knee injury sustained during the record 58-10 defeat in Bloemfontein.
It will be the second time World Cup winner Wilkinson has led his country, and he will skipper a side showing six changes and one positional switch from a week ago.
Newcastle centre Jamie Noon will play on the right wing in place of Iain Balshaw, while Saracens' Dan Scarbrough steps in for Robinson and makes a first England appearance for almost four years.
As expected, Bath prop Matt Stevens is preferred to Stuart Turner, with Bristol Lock Roy Winters partnering Alex Brown in the second row, while new cap Ben Skirving will wear the number eight shirt, with Magnus Lund replacing injured openside flanker Andy Hazell.
A reshuffled back-row sees Nick Easter switching to blindside, while Harlequins full-back Mike Brown has made an unexpectedly quick recovery from the stomach virus that has affected several England players on tour.
Brown was formally ruled out of the running by England head coach Brian Ashton two days ago, but he has been declared fit to retain the number 15 jersey.
Bath full-back prospect Nick Abendanon, who only arrived in South Africa yesterday, will be on the replacements bench.
Johannesburg-born Abendanon, 20, has impressed for his club this season, and is rated by many judges as having an outstanding chance of making the World Cup squad.
The England bench includes four players from Sale, with Turner, Chris Jones and Dean Schofield all dropping down from the starting XV on duty in Bloemfontein.
England are striving to avoid an eighth successive away defeat, while they have not won in the southern hemisphere since the 2003 World Cup final.
But they are unlikely to end either of those sequences, with South Africa red-hot favourites for another landslide success.