Flood’s call-up is one of five changes – two positional – that have been made to the side which lost the first Test 22-17 in Durban last weekend.
Inside centre Brad Barritt has been ruled out due to surgery on a lacerated eyeball, with Manu Tuilagi, who was outside centre, shifting into the number 12 jersey.
Jonathan Joseph, who was Barritt’s replacement when he left the field in the second half last weekend, will replace Tuilagi at outside centre and make his first Test start.
Fullback Mike Brown, who was sent home earlier this week due to a fractured thumb, has been replaced by Ben Foden, who was left wing in the first Test.
David Strettle, who was impressive during the Six Nations campaign, returns to the number 11 jersey.
“There will be a different emphasis in terms of the personnel that have been picked, but playing in the right areas is still first and foremost. We don’t want to expend too much energy playing in our own half,” England coach Stuart Lancaster told a news conference in Johannesburg on Thursday.
The 20-year-old Farrell’s goalkicking was impressive during the first Test but he only used his backline sporadically. Flood is expected to provide more vision and attacking spark to the backs.
“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,” Lancaster said.
“Toby will form a Leicester triumvirate with Ben Youngs and Manu Tuilagi and hopefully they can bring that synergy at club level into the test.
“Having two ball-players in the backline is important for the balance, but we have to prepare for both attack and defence, and recognise the threat the Springboks pose through the midfield channels. We have to win the gain-line battle and we have a better opportunity of doing that with Manu more able to get over when he’s playing one place inside. If he gets over the gain-line, then hopefully the two ball-players outside him can capitalise,” Lancaster said.
England’s starting pack, which was outplayed by the Springboks in the second half, remains unchanged, but reserve prop Paul Doran-Jones has been replaced by fit-again Alex Corbisiero on the bench.
Joseph’s place on the bench has been taken by Alex Goode.
“Jonathan is exciting, he has good feet and is a good distributor, plus he has the temperament to play at this level,” Lancaster said.
Team – 15-Ben Foden, 14-Chris Ashton, 13-Jonathan Joseph, 12-Manusamoa Tuilagi, 11-David Strettle (Saracens), 10-Toby Flood, 9-Ben Youngs, 8 Ben Morgan, 7-Chris Robshaw, 6-Tom Johnson, 5-Geoff Parling, 4-Mouritz Botha, 3-Dan Cole, 2-Dylan Hartley, 1-Joe Marler. Replacements: 16-Lee Mears, 17-Alex Corbisiero, 18-Tom Palmer, 19-Phil Dowson, 20-Lee Dickson, 21-Owen Farrell, 22-Alex Goode.