It was Jones' second World Cup silver medal, while he also won gold as an assistant coach with South Africa in 2007.
"I don't know why we didn't play well today and this is one of the things that happens in high-level rugby," he told media afterwards.
"We thought our preparation this week was good but in the end it wasn't because we didn't play well. You can have the most investigative debrief of your game and you still don't know what was wrong.
"We got in trouble in the scrum. We struggled in the first half, made some personnel changes in the second half and got back into it," he said.
"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.
"You have got to be able to break the game open a little bit, you have got to be able to stay in the fight, and then when you get the opportunities to break the game open.
"We stayed in the fight and 50 minutes into the game we were in with a chance, but we failed to take our opportunities. For some reason South Africa were too strong for us. They took their opportunities, and that was the difference in the game," he said.
Jones said there was no doubt about the effort of the players who had been extraordinary. They had played with a lot of pride and passion and he didn't know why they had come up short.
"Sometimes you never know," he said.
"We're going to be kicking stones for four years and it's hard to kick stones for four years.
"We're massively disappointed but at the same time I've got great admiration for what the players did. I can't tell you how much respect I've got for them, how hard they've worked, how well they've played but we came short today. But it's not because of lack of effort," he said.
Jones declined to talk about his future and intended to get over the next few days before considering that.
"We're the second best team in the world. We didn't meet our goal, our goal was to be the best team in the world, and we're the second best team in the world. So that's how we should be remember," he said.
South Africa were worthy winners. They played very well and were too good for England 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," he said.
Captain Owen Farrell said: "At the start they had a lot of ball in the right areas and put us under pressure. After the first half we came in thinking we hadn't fired a shot.
"In the second we felt like we were in a game and got some momentum, but not enough. We couldn't get a foothold, but they are a brilliant side and played brilliantly today."