"It's obviously a huge disappointment [to lose] but we left ourselves a huge mountain to climb going into the last quarter," said Jones after the Boks had taken a 26-7 with 33 minutes remaining.
He added: "Looking at the positives, we created a few opportunities but we hadn't been clinical and we didn't take the chances until the last quarter. I thought the centres played particularly well, creating a lot of problems. Our pattern worked and our fitness levels were good - these are the areas that are good for us and we can look to take them into the next game but there are areas that we need to address as well.
"As the game progressed I thought we grew into the game and we managed to get the ball through our hands a bit quicker, we were more efficient in the contact area and we created more problems and I thought our energy levels were good as well."
The Welsh star admitted the Lions took time to hit their straps as the Boks hit the ground running.
"They started very well and got a lot of points on the board early and that made life difficult for us and silenced the crowd and we didn't get much momentum then.
"I was happy with the way we were played in the second half, the speed of the ball was good, we were playing with a lot of width in our game and I thought we were causing a lot of problems but we left ourselves too big a challenge.
"We showed character and belief and when we do implement the game plan it works and that is our big challenge that we need to play not just for sections of the game but the whole eighty.
"We are lucky, if this was a World Cup final that would be it, the tournament would be over but we are fortunate that we have another opportunity this Saturday to get level in the series. We take a lot of heart from the fact that when we play, we can play some good rugby and cause problems and that is how we have to go into this game.
"But we have to be honest with ourselves, work hard this week, address areas where we are not so clever at the moment. We are all in the same boat (backs and forwards), the backs have to look at areas of our game where we need to be more clinical and areas that we need to address, yes from a positive we are creating the opportunities but we need to finish them off."
Meanwhile, Lions doctor James Robson has confirmed the injuries in the squad.
"Tommy Bowe suffered a slight strain to his elbow in yesterday's game but should be fit for selection for Tuesday if that's the want of the coaches. Lee Byrne strained his foot during the game. With it only 12 hours after coming off, we have only done our initial assessment and the aim at the moment is to get him to the point where he is fit for selection on Tuesday.
"It is probably a mild recurrence of a previous injury - plantafasciotous or inflammation or tearing of the structure that holds the arch of the foot principally - it is a very painful and often recurrent condition but he has played well on this tour it may have well been that he has pulled a few fibres but he is certainly walking around fine this morning.
"Tom Croft strained his calf during the game and a few hours later appeared to have a bit of a twisted knee but has improved massively over night and has done a very good pool session while Gethin Jenkins has a bit of a black eye this morning and has had four stitches to his eye for a cut.
"James Hook continues to make excellent recovery from his head knock last week and he has been doing some further testing this morning - he's now done various grades of activity with no ill effect, he's done non contact rugby activities with no ill effect and we have high hopes for him to be passed tomorrow.
"He is of course subject to an independent neurological assessment which takes the decision out of our hand as per IRB regulations. The assessment takes place tomorrow ahead of selection for Tuesday and at each step he has progressed well."