But spirited Wales kept fighting with George North grabbing a second try and they hammered away at the South African try-line deep into injury-time.
"There's a great team spirit in terms of the effort the guys are putting in and we want to be successful," said Jones.
"OK, certain things aren't happening at the moment, but we'll keep giving it our best and keep knocking at the door until it does happen.
"It's just frustrating at the moment that we are nearly there, but just can't seem to close out games.
"We are realistic where we are at. We've got self-belief in the squad. We know when we play to the best of our ability we can cause problems. That was evident out there against the Springboks.
"In some patches we were good with the ball. We were efficient in our recycling, we put the ball through our hands quickly, we played with a lot of width and got our game-breakers into the game and that's the way we want to play.
"We just have to play that rugby for longer periods and hopefully that victory will come along."
The Scarlets play-maker admitted Wales were disappointed at the 25-16 loss to Australia and wanted to bounce back with a big performance against the Springboks.
"We were disappointed with last week's performance against Australia and wanted to give an enthusiastic and energetic performance.
"I felt we did that. It was a spirited effort. We made a great start and played some really great rugby in the first half.
"But that first 20 minutes of the second-half was hugely disappointing. Obviously we have got to give South Africa credit for the way they played in that period.
"They were very efficient, they carried the ball very well, they were very direct. It was a simplistic game-plan but very well executed and made our life very difficult.
"We are hugely frustrated not to have won the game. We gave it our best shot."