Daly's kick on his first start, and the excellence of his performance, was another symbol of Jones's transformation of this England side.
'There's a blaze of light in every word,' the half-time soprano sang from the late Leonard Cohen's lyrics to Hallelujah as England's players sat in the dressing room, listening to their coach. Right now he is the man who can do no wrong.
It is not as if Joseph had performed poorly, but Jones picked the Wasps centre in his stead anyway.
He is selecting now from a position of strength, a luxury he has earned with the success he has wrought since he took over as England coach in the aftermath of a disastrous World Cup last year.
Jones is the man with the Midas touch. Next weekend, it will be a year since he was appointed as England's first overseas head coach in succession to Stuart Lancaster and the success he has brought has exceeded the wildest of expectations.
This crushing 37-21 victory over the Springboks was the tenth win in a row since Jones took over - the first time an England coach has done that - and his team appears to be getting stronger and stronger. It is their longest winning run for 12 years.
It was also the first time England had beaten South Africa since a 23-21 victory at Twickenham in November 2006.
After completing the Six Nations Grand Slam last spring and recording history-making victories over Australia in Brisbane, Melbourne and Sydney in the summer, Jones is ridding England of their inferiority complexes one by one.
But Jones does not rest. And Jones is never satisfied. He was displeased with some of the penalties they gave away. He said England deserved a 'pass mark' but no more.
He is a relentless taskmaster and that is one of the reasons England have improved so dramatically during his tenure.
When he was asked if his year in charge had surpassed his own expectations, it was all he could do to suppress a sneer. "When I took the job, I had no expectations," said Jones.
"All I knew was that I was inheriting a very good side that was put together by Stuart Lancaster that had oodles and oodles of talent. My job was to make sure that talent produced performances.
"We're starting to do that but we've got to get better. We're nowhere near good enough at the moment."
What an effect he has had. England are the second best team in the world behind the All Blacks and the momentum is with them.
Watching England at Twickenham is a hot ticket again and the team is steaming fast towards the World Cup in Japan in 2019 with the intention of completing this comeback and slaying the ghosts of last winter.
It is a thrill to watch them now, just as it was when they were heading inexorably towards World Cup glory in 2003.
The team have an air of certainty about them again. The crowd does not hope any more. The fans expect. England are hobbled by injuries to important players at the moment but you just would not know it.
Gone now is the huge disparity between southern and northern hemispheres that appeared so firmly entrenched at the last World Cup.
Jones led the way out of that with that first-ever series victory Down Under and Ireland followed it up spectacularly with their 40-29 victory over mighty New Zealand at Soldier Field in Chicago last weekend.
England have performed consistently enough now to prove that they have gatecrashed the southern hemisphere party. They deserve their No 2 ranking in the world and they were utterly dominant against the Boks, who added a little respectability to the scoreline with a late try from Willie le Roux.
Saturday's defeat marked the first time since 2010 that South Africa have lost six matches in a calendar year.
They are going one way. England are going the other.
No one is complaining any more about the unforgiving training camps that Jones organised in Teddington, Brighton and Portugal and the injuries that occurred there. They were collateral damage on Jones' relentless march forward, that's all.
His intensity, what he demands, is a big part of the reason why England are now where they are.
Before he left the stadium last night, Jones was invited to pat himself on the back about the selection of Daly. He declined. He made a joke instead.
"He's got an educated left foot, hasn't he," he said. "You can tell he has been at public school."
