Barca's loss represented their heaviest defeat in European competition and Messi conceded that the odds are against the Catalans turning the tie around at Camp Nou next week.
"It's 4-0 and it will be difficult because they are a great team," Messi told reporters.
"They were a lot stronger than us – physically superior in fact. It's a disgrace what happened, but we have to go on.
"We'll try to score at home and do our best. We must go on. Now we must win la Liga soon."
The Argentina international had not featured for the Blaugrana since making a rapid return from a hamstring strain to lead his side into the last four at the expense of Paris Saint-Germain on April 10 and he seemed to struggle to get into the game against Bayern.
However, he dismissed the suggestion that he should not have been risked in the first leg.
"It was some days since I played and I didn't feel 100% comfortable but I was not injured, so I could play," the 25-year-old insisted.
Meanwhile, Messi's team-mate Gerard Pique was distraught with his side’s showing in Bavaria, but admitted that the visitors had come off a clear second best.
"They were quicker, stronger and played better football," the centre-half told TV3. "They were the superior team.
"[Winning the tie] is almost impossible. We will have to turn around and go out and win the next match for our fans.
"We have been given a refresher."
Mario Gomez appeared to have been offside when he slotted home Bayern's second goal, while Thomas Muller fouled Jordi Alba in the build-up to Arjen Robben's goal moments later.
However, Pique did not want to lay the blame on officials for Barcelona's humiliating defeat.
"The referee did not have any influence on the result," the former Manchester United defender stated.
The second leg will take place at Camp Nou on May 1.
