Coach Fabien Galthie had made 12 changes to the team who beat New Zealand in the tournament's opening match and the reserves failed to rise to the occasion.
"Fifteen penalties is huge. It's unacceptable at international level, we're lucky to win after being penalised so many times," said Woki, who started against the All Blacks in a match France finished with only four penalties against them.
"We had worked hard (on discipline). We wanted to do something good and we just showed we were an ill-disciplined team.
"It's very frustrating. We struggled in the scrums, we knew we were better but then we were not patient. We have to be patient."
France, who lead Pool A with eight points, next face Namibia on 21 September.
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