Daly, who has won five caps as a replacement, has got the nod to start at outside centre for tomorrow’s autumn series opener against the Springboks at Twickenham.
The Wasps centre will form a new midfield partnership alongside Owen Farrell that offers long-range left- and right-footed kicking options.
“JJ has missed a little bit of training lately and I just feel that Elliot is a bit sharper at the moment,” said Jones, when asked about his decision to select Daly ahead of Joseph, who drops to the bench. “He (Daly) has got pace and power and a booming left foot, which can be very useful, and he has done well in Tests when he has come off the bench.
“JJ is a great team player and he will be back.”
Daly was among the Aviva Premiership’s most dangerous players last season with his acceleration and eye for an outside break terrorising defences to Wasps’ benefit.
While Joseph relies on elusive footwork and a burst of speed to beat defenders, Daly’s skill lies in gliding through gaps and he also provides a long-range boot out of hand and from the kicking tee.
Injuries have given Northampton flanker Tom Wood a chance to end a year-long spell in the international wilderness that began after last autumn’s World Cup.
Wood has been picked at No 7 ahead of Nathan Hughes, with Jones opting for his work-rate, line-out expertise and experience over the explosive potential of the Wasps back row.
“South Africa rugby is about big ball carriers and playing off the back of that,” said Jones.
“Tom has got a big role in that area – to stop their ball runners. He has got a good workrate and he can stop them on the gainline.”
England captain Dylan Hartley said his Northampton team-mate had earned his recall.
“Tom has been out in the wilderness, but he has got his head down and worked really hard and it has paid off. His work ethic is unbelievable.”
South Africa have lost five of their past nine matches and England will be hoping they can end a run of 12 matches without a win against them that stretches back to 2006.
“We are an ambitious team and we want to be the No 1 team in the world,” said Jones. “This game against South Africa is another step towards that and we are looking forward to it.”
Hartley’s Northampton team-mate Courtney Lawes will win his 50th cap having made his debut against Australia at Twickenham in 2009. Hughes is one of three uncapped players featuring on the bench, with Harlequins tighthead prop Kyle Sinckler and Worcester centre Ben Te’o are also set to make debuts.
Wing Jonny May also makes his first appearance since the World Cup following a year-long battle with injuries, lining up on the left with Marland Yarde patrolling the opposite flank.
There are six changes to the starting XV that toppled Australia 44-40 in June.
England: M Brown (Harlequins); M Yarde (Harlequins), E Daly (Wasps), O Farrell (Saracens), J May (Gloucester); G Ford (Bath), B Youngs (Leicester); M Vunipola (Saracens), D Hartley (Northampton, capt), D Cole (Leicester), J Launchbury (Wasps), C Lawes (Northampton), C Robshaw (Harlequins), T Wood (Northampton), B Vunipola (Saracens).
Replacements: J George (Saracens), J Marler (Harlequins), K Sinckler (Harlequins), D Attwood (Bath Rugby), N Hughes (Wasps), D Care (Harlequins), B Te’o (Worcester), J Joseph (Bath).