But he had no complaints on a day when South Africa dominated every critical area – notably the scrum – and took their chances in a 32-12 victory.
Stand-off Handre Pollard kicked 22 points, while wings Makazole Mapimpi and Cheslin Kolbe scored late tries to destroy England’s bid for a first world title since 2003.
“You can have the most investigative debrief of your game and you still don’t know what was wrong,” Jones said. “It just happens sometimes.
“It’s not a good day for it to happen.
“We are going to be kicking stones for four years, and it is hard to kick stones for four years, so we are massively disappointed.
“At the same time, I have got great admiration for what the players did. I can’t tell you how much respect I have got for them.
“That wasn’t the outcome we expected. They were worthy winners, they played very well and were too good for us on the day.
“We struggled to get into the game, and when we had opportunities we didn’t take them. It was just one of those days when South Africa were too good for us.”
England lost prop Kyle Sinckler to a third-minute head injury, and his replacement Dan Cole was given a torrid time by opposite number Tendai Mtawarira.
“He is recovering and will go through all the head injury protocol,” Jones said, of Sinckler.
“You have 23 guys, you lose a guy early and you have got to be able to cover it. I don’t think that was a significant factor in the game.
“We got in trouble in the scrum – we struggled particularly in the first half.
“We made some personnel changes in the second half and got back into it, but South Africa for some reason were too strong for us.
“We didn’t think that was going to be the case going into the game, but that’s how it happened.
“That’s what happens in rugby sometimes.”
Reflecting on England’s World Cup campaign, Jones, inset, said: “We didn’t meet our goal to be the best team in the world, but we are the second-best team in the world, so I think that’s how we should be remembered.
“The only thing I am worried about now is having a few beers.
“And then after we have a few beers today, we will probably have a few more beers tomorrow and maybe Monday, and then maybe we will have to pull up stumps.”
England captain Owen Farrell, who kicked all of England’s points, said: “We probably came in at half-time thinking we had not fired too much of a shot.
“The second half was a bit different, it felt like we got some momentum, but probably not enough, and then off the back of it we got caught again and they got the momentum straight back.
“In terms of the start of the game, they had a lot of ball in a lot of the right areas and seemed to get a good few calls, and that put us under pressure.
“We didn’t seem to be able to get a foothold in the game, and they had a lot of momentum in the first half.
“They are obviously a brilliant side, and they played brilliantly today.”