The Argentine maestro scored PSG's second goal as they ran out 2-0 winners at the Parc de Princes.
"We know it's impossible to control Leo during 90 minutes but he was not much in touch with the ball," said Guardiola.
"He was coming back from injury but we know quite well when he can run and get close to the box he is unstoppable. We did quite well to reduce those chances."
Guardiola also wished Messi the best after scoring his first goal for PSG, adding: "I wish him the best, if he is happy and enjoying this period in Paris I will be happy.
"He decided for many reasons to come here, for him and his family. I wish him the best."
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