Skelton, who suffered a calf strain, and Tupou, who was ruled out with a hamstring problem, were key to Jones's plan of combining forward power with backline flair in Australia's key Pool C matches against Fiji and Wales, both of which were lost.
"The biggest loss we had in this tournament was losing Taniela and Will in one session and I blame myself for that," Jones told reporters at the team camp outside Saint Etienne on Friday.
"Just didn't get it right, the session. You never know with injuries, you never really know. But could we have done that a little bit differently? I keep thinking about that.
"To minimise the risk of damage, there's just an order of training and the way you train. I hold my hands up."
Skelton intervened at this point to disagree with his coach.
"You can look at anything, if I had a half an hour more sleep, if I had drunk a litre more water. I think for those things, I'm in control," he said.
"Things happen and that's rugby, injuries happen during the week and in games. I (might) have got injured on the weekend against Fiji. It's unfortunate and I guess we've got to move on."
NO EXCUSES
Jones said he was not trying to make excuses for Australia's poor showing at the tournament and said a better team would have been able to win without Skelton and Tupou.
"We've got to be good enough to cope with it," he said.
"They're the challenges of being a good team, the world's best teams get on with it. And we're not quite there yet. And that's the challenge. The challenge was to fill that gap to be able to cope with those situations."
The Wallabies have remained in France despite having completed their pool matches as a win for Portugal over Fiji on Sunday without the Pacific islanders earning a bonus point would send Australia into the quarter-finals.
Jones reiterated that he took full responsibility for the disappointing campaign and said he would honour his contract until the end of 2027 if Rugby Australia did not sack him in the wake of a post-tournament review.
"This team is going to be a good team," he said. "We need one or two quality players to add to it. We're not the finished product yet..."
Skelton and Tupou, he added, would be fit to play if Australia did squeak through to the knockout stages.
The team announced earlier in the week that fly-half Carter Gordon and lock Nick Frost had been ruled out of the remainder of the tournament by injury.
