The home side led 12-3 at the point where Jamie Heaslip was sin-binned early in the second half, and were taken apart in his absence. Heaslip was captaining the team for the first time, and South Africa prevailed 16-12.
Pienaar crossed for the only try of the match in the 45th minute and Pat Lambie kicked 11 points as South Africa, who started as strong favourites, took control.
Pienaar, who plays club rugby for Ulster, said: "I think we had a terrible first half. Our kicking game wasn't that great. In the second half our forwards made a huge step up.
"We got a couple of good drives going, kept the ball and forced them to make errors. I'm very proud of the guys, especially in the second half."
Asked if there was any sense of concern that South Africa had managed just one try, Pienaar said on BBC2: "Not really. It's a hard place to come and play rugby. It's a good Irish team.
"To get just one try is the least of our concerns."
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