England were leading 13-9 with 12 minutes left before tries by Cory Hill and Josh Adams gave Wales a victory that kept them on course for the Grand Slam.
"It was a nip and tuck sort of a game, fine margins, you make one mistake it cost us a try that ultimately cost us the game,” Jones told reporters.
"We started the second half brilliantly but lost a bit of momentum and gave away some penalties, which allowed them back in the game. They beat us in the air, the penalty count was lopsided and when you are getting beaten in those two areas when it's a tight game, you are going to struggle," Jones added.
"Full credit to Wales, they played very well, deserved to win today, played smartly, and we just let ourselves down in the areas I spoke about."
Jonathan Davies (L) celebrates as Josh Adams of Wales scores their second try
Image credit: Getty Images
Jones accepted that the extraordinary pressure-cooker atmosphere in the last quarter helped the hosts.
“It always plays a part…I think when you are under pressure all the time, players tend to do things they might not do normally and we could have been better in that area,” he said.
“You've got to be good enough to cope with it and today we weren't quite good enough and there's no embarrassment to that. We'll get better and we'll learn from that and we'll be right."
England are still in a strong position to win the title – assuming Wales don’t beat Scotland and Ireland to complete the Grand Slam.
The bonus points earned against Ireland and France alongside remaining home fixtures against Italy, who have never beaten England, and Scotland, who last won at Twickenham in 1983, mean they would probably be crowned champions if Ireland beat Wales on the final day.
“We’ll lick our wounds and get ready for Italy,” Jones said. “Beat Italy, we are in the last round and we'll see where the land lies. Wales are a bloody tough side, they have a good chance of winning the Six Nations but we’ll be chasing them, they have a couple of hard games coming up."
Jones was also supportive of prop Kyle Sinckler, who tackled magnificently but also gave away the two second-half penalties that allowed Wales to close the gap. The referee put the prop on a warning and Jones acted quickly by hauling him off.
“Every time you make a change there’s a number of factors involved,” he said. “He was starting to get a little bit tired. I know you guys want to single him out because Warren said what he said but don’t be unfair to him, boys. He’s a young player on the way up. Look after him a bit.”
Captain Owen Farrell also bemoaned the way England dropped off in the second half – when they scored only one penalty.
“The most disappointing thing from a players' point of view is that we didn't get much momentum towards the end of the game so it will be about how we wrestle that momentum back,” he said.
Farrell will remain sole captain for the remainder of the tournament after Jones confirmed that co-captain Dylan Hartley, who has not played since before Christmas, would be having knee surgery on Tuesday and would be out of action for around three months. (Reporting by Mitch Phillips, editing by Ed Osmond)