Ricardo Quaresma twice punished Bayern mistakes in the opening 10 minutes at the Estadio do Dragao as Porto took a commanding lead.
Bayern did claim an away goal through Thiago Alcantara shortly before the half-hour, but Jackson Martinez - returning from a thigh injury - took advantage of another defensive slip to restore the two-goal cushion midway through the second half.
"It [the second leg next week] will be a very difficult match, we are still half through this round, against one of the greatest teams in Bayern history," Lopetegui said.
"We were great tonight and I want to congratulate this group of players. This team has lots of ambition.
"Jackson gave good indications yesterday and we decided to take the risk. The game in Munich will be different and we will not be able to count with two important players [the suspended Danilo and Alex Sandro], so we will have to find solutions for that problem.
"Playing against Bayern is always difficult, but we made a great start in the match against the greatest team in the world in terms of possession.
"In the first half maybe we should have had the ball with us for longer, but we corrected that in the second half."
Two-goal hero Quaresma, meanwhile, was quick to shift the praise onto the rest of his team-mates.
"This is a night for me to remember, but more important than my performance was our victory," he said. "We knew we were facing a great team, with great players, so we have to be happy.
"We all work a lot and when we win, we all win. I only do my job, I am in a good moment and so is the team. Now we will first think in the match against Academica [in the Primeira Liga on Saturday] and only after that game we will think about Bayern again.
"[Manuel] Neuer is one of the best goalkeepers in the world, I respect him a lot, but when I came face to face with him I only thought about scoring. We are all vital elements in our team."
