Leading 3-1 from the first leg in their UEFA Champions League quarter-final, Porto travelled to Munich with high hopes of finishing the job.
But a devastating attacking display from the hosts put paid to that, as Bayern scored five times in the first half to put the game out of sight.
Porto did pull one back through Jackson Martinez, but Ivan Marcano's red card and Xabi Alonso's late free-kick completed their misery.
"We were lacking three important players [Danilo, Alex Sandro and Cristian Tello], but that does not justify everything," Lopetegui said.
"We started the match very badly against a Bayern side that is very strong offensively, both individually and collectively - even more so when they are playing at home - and in the first half they were able to settle the match and the qualification for the next round.
"In the second half we were better, we were able to have more possession, something we couldn't do in the first period. When that happens you are always going to be punished.
"Against a team like Bayern you have to be at your best during the 90 minutes and we were not able to do that. Congratulations to Bayern.
"We are sad, but we made a great campaign in this Champions League. In 11 matches this was our only defeat.
"We knew it was always going to be a difficult match and we made a lot of mistakes in the first half.
"But in the second period we showed that without those mistakes we could have fought for qualification. Now we have one competition left to win [the Primeira Liga] and we will do everything to win it."
