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The hosts were beaten 27-13 at Twickenham as the world champions dominated the set-piece.
Head coach Jones apologised for the performance but said his players were still heading in the right direction, 10 months out from the World Cup.
“We are disappointed we didn’t play how we wanted to,” Jones told Amazon Prime.
“South Africa do things to you that are sometimes difficult to deal with.
“We didn’t land a shot like we wanted to. You have to win contests and we didn’t win in the air or the set-piece, so it’s hard to get in the game.
“We lost two of the key contests but we will improve in those areas. Results tell you everything and that is what we are judged by but I feel like there is growth in the team, which we have seen, but wasn’t evident today.”
Jones’ side have lost six of 12 Tests in the calendar year, England’s worst run since 2008.
Defeat by the Springboks followed a comeback draw against New Zealand, a victory over Japan and a defeat by Argentina in a disappointing autumn schedule.
Asked if he was still confident in his ability to lead the side into next year’s World Cup in France, Jones said: “I think about where we are going towards a World Cup.
“Obviously we want to win games and be successful but are we moving in the right direction? Yes we are.
“I have coached for a number of years and I believe I can coach well. People will say what they say, and there are ups and downs in sport but we didn’t play well today and I apologise for that, it’s entirely my fault.”
He added: “Obviously on results, we are not happy but I feel like we are building a really good base to have a really good go at the World Cup, a really good go.
“A number of young players got great experience today and they’ll come back better players for that. We’ve got other players coming back to form, some of our more senior players and we’re not far away.
“We need to develop consistently. Test match rugby is all about consistency.” – BBC Sport.
Mathew Masinge
Online Reporter