The Spanish giants suffered a surprise 4-0 loss in their first leg of their UEFA Champions League semi-final and are now facing a huge uphill challenge to qualify.
Messi was a peripheral figure at the Allianz Arena and did not look as if he had recovered from the hamstring injury he suffered a just few weeks ago.
But the Argentine said: "I felt good. I was well enough to play. We have to lift ourselves for the second leg and La Liga. We will bounce back.
"They were a lot stronger than us, physically superior. It is a pity what happened but we have to move on."
Midfielder Xavi also remains adamant Barcelona have not given up hope of reaching the Champions League final at Wembley despite the odds being stacked against them.
"We are Barca and we have got to try to get to the final," said the Spaniard. "We need to play a great game but we know at the same time that it is practically impossible."
Xavi paid tribute to a Bayern side who outplayed and outmuscled the 2009 and 2011 Champions League winners like very few have achieved over the past six seasons.
"They were quicker than us and it was like a siege," he said. "We expected it to be like this. They are very strong physically and they were better than us.
"When you make mistakes in the Champions League, you pay the price. They were stronger than us. I do not know why we did not attack well.
"They have extraordinary players like (Arjen) Robben and they just found it too easy to get past us."