By Peter Staunton at Estadio do Dragao
Julen Lopetegui's side stormed into a 2-0 lead at the Dragao thanks to two early goals from Ricardo Quaresma and, though Thiago Alcantara pulled one back, Jackson Martinez rounded off the win after the break.
Muller lamented his side's slow start to the game but was less than impressed with what he saw as a negative approach from the hosts.
"Everyone could see how we did not exactly start well," he said after the game.
"I think we did pretty well after going 2-0 down until half-time. We controlled the match, had some good moves and made it 2-1.
"We didn't give away any chances, except for a header after a free kick right before the break. At half-time we thought we could do better.
"Porto did a good job of parking the bus. What was disappointing is how we weren't able to keep the match calm. There were many fights and fouls in midfield.
"It was lively and that wasn't good for us. And the worst thing was conceding the third goal."
Despite the result, Thiago's strike means Bayern remain in the tie and Muller is still confident of turning the game around in the second leg at the Allianz Arena.
"We are still Bayern and we will play at home. Of course we cannot give away goals again. But it's not like we've never won at home before. We still believe but we're aware that we can't play like that again.
"This is football. If you make mistakes, it can cost you. And that happened today. We had a totally competitive team out on the pitch. But any match gets difficult when you conceded early goals like that.
"It wouldn't be a miracle if we win 2-0 at home. But there is certainly a lot of work to do and it won't be a piece of cake. We made it tough for ourselves with this result, but at least we got an away goal."
Bayern will seek to overturn their first-leg deficit at the Allianz Arena on Tuesday at 20:45CET.