The German centre-back was the ridicule of numerous internet memes having been deceived by the Barcelona ace in their Champions League semi-final encounter in May, causing him to fall over.
The 26-year-old has laughed off the incident, insisting it hasn’t affected him, before hailing Messi as “the best player in the world”.
"That doesn't really affect me," he told ESPN. "I was laughing at myself. When you fall down or slip in a situation and somebody scores a goal, it's normal. These things happen; it happens to me, it happens to other players, I don't care about these things.
"For me, he's the best player in the world. That's football. Sometimes you look bad or something happens. I'm a defender, that doesn't kill me or anything."
Bayern were undone 5-3 on aggregate by the eventual European champions, but Boateng hopes his side will be able to challenge once again next season.
"Of course it was a bad loss for us, and we did well for 75 minutes or something, and then against a team like this it's difficult," he said.
"Especially the second goal was a great goal from Messi. At the end of the day, you have to continue your hard work, and next season I will try with the team again to win the Champions League. Sometimes you lose, sometimes you win, sometimes you are unlucky, but that's life."
Bayern coach Pep Guardiola has come under fire in certain media for only delivering the League title this past season, yet Boateng has defended his manager and is looking forward to working with him again in the new season.
"For me, [Guardiola] is one of the best coaches I've ever met,” he said. “He's super clever and tactically really good, and he knows how to speak to us, how to motivate us and that's what it is like. He's a really great coach and I'm really happy I can train under him.
"Now, I'm looking forward to how he is going to prepare us for the new season. It always interesting because he's always coming up with new ideas. He always wants to make every player better everyday and I'm really interested and excited to see that."