The Argentine forward turned Boateng inside out in Wednesday night's UEFA Champions League semi-final first leg, when he netted his second goal in Barcelona's 3-0 win over the Bavarians.
Boateng was embarrassed after Messi changed direction at lightning pace, causing the German international, who is of Ghanaian decent, to plumet to the ground and allow him to double Barcelona's lead in the 80th minute.
The 26-year-old rejected personal criticism and said the 3-0 final score was a result of the team's failure to maintain their defense at the dying stages of the match.
"You can't keep Messi out of the game for 90 minutes. We did really well to limit his influence for the first 70, but then you have to continue to defend as a team.
"After falling behind, which shouldn't happen in the first place, you can't then allow the other team to further increase their advantage," he concluded.
Pep Guardiola's side will have a mountain to climb in order to overturn a three-goal defecit when they welcome the Catalan giants to the Allianz Arena for the semi-fianl second leg on May 12.