His side looked in a commanding position at 16-3 but the Springboks showed why they are the leading side in the world with a relentless fightback which saw them roar to a 31-19 lead before Wales hit back with a late try by Alun Wyn Jones as the match reached its climax.
But it proved a missed opportunity for Wales who were playing a Springboks side missing several top line players including Bryan Habana, Pierre Spies and Bakkies Botha, as Gatland conceded.
“We are frustrated,” said Gatland. “If that was a couple of years ago we would have said what a good performance it was. But we have come on from there. In the opening 25 minutes we were clinical, accurate and 16-3 up, and then we caught some sort of disease, I don’t know what it is.
“We got ourselves in a bit of trouble, got behind and then showed great character at the end. But we are frustrated at a missed opportunity.”
He added: “We played the world champions today. Guys who played in the Super 14 final last week, and the Stormers and the Bulls are two of the best teams in the world.
“The thing from today is you feel like you are not too far away and you are not turning up thinking we hope to have a good day and they have a bad day and we can cause an upset.
“We know if we are more clinical we are capable of beating anyone. Today was an opportunity we didn’t take. As a team you grow and mature and learn to handle situations and sometimes it’s about a bit of luck getting that win can transform a side’s confidence and belief.”
Gatland was disappointed his players took their feet off the throats of the prone Springboks are jumping out to a 16-3 lead.
“We just went through a poor period and of course the other side will come back into the game. We lost three line-outs in a row, we had a couple of turnovers at the breakdown and at 16-3 we gave away a stupid penalty through Jonathan Thomas that gave them a bit of momentum.
“We also missed a couple of tackles and it was disappointing. But we showed some great character to give ourselves an opportunity of winning it.”