The converted score ultimately ensured the Boks got their UK tour off to a winning start but skipper Smit feels it also affected his side in an adverse manner.
"We made it tougher than we should have," said Smit.
"We took our foot off the pedal after the intercept try of Jean's. We all thought it was just going to happen from there and we went into the wrong frame of mind and defended what was a small lead."
Wales registered 12 unanswered points after de Villiers' score to peg the Boks back to just a five-point advantage and Smit feels his side must take responsibility for not building on their lead.
"That was a defining moment for us. A guy with Jean's vision is always going to get one or two of those. Bryan Habana's the same - we've got those kind of players that will make that break.
"When Jean went through, we knew it was try time so we had quite a lot of time in the middle to talk and I said, 'lets make that the beginning of the kind of momentum we want to create'. Seven points took us 17 points ahead and I said to the guys, 'now lets use that buffer to start playing some rugby'.
"But we didn't get out of our half accurately. We made some mistakes and put the pressure on. I think we'll feel it tomorrow, the amount of work we had to put in in defence, because of that.
"There was a little bit of rust and we will certainly have a lot to work on next week."