The 2013 European champions began Wednesday's first-leg clash at the Estadio do Dragao in disastrous fashion, handing their opponents two goals in the opening 10 minutes.
First, Xabi Alonso was robbed of the ball by Jackson Martinez, who was then fouled by Manuel Neuer before Ricardo Quaresma netted the resulting penalty.
Quaresma then dispossessed Dante and ran clear to score a second, and although Thiago Alcantara pulled one back, Jerome Boateng's misjudgment let in Martinez to round Neuer and slot home after the break, leaving Bayern with it all to do in next week's return leg.
"We were prepared for Porto's pressing, but that's football on the highest level," Sammer said.
"Their third goal also results from an individual mistake by us, which is quite annoying. We could have lived with a 2-1 defeat, but now we really have to shake this off.
"Next Tuesday we are playing at home and we have to deal with this setback until then. If you want to be a great team, you have to be able to come back from this."
"Their third goal was a setback for us, but mistakes happen in football," Thomas Muller added. "If you make a mistake in defence, it has other consequences than making a mistake up front.
"It's a risk we are willing to take. Now we have to win 2-0 at home to go through. The result is always tied closely to the performance.
"We got off to the worst possible start, but overall we weren't that poor in the first half. Then Porto were very defensive minded."
Captain Philipp Lahm, meanwhile, said Bayern's approach can sometimes lead to conceding goals in such fashion.
But he has warned Porto that the tie is far from over.
"We always want to build up from the back and this style can be dangerous," he conceded. "We can't make any accusations though. Mistakes happen.
"We were looking good when pulled a goal back, but when Porto made it 3-1, that really hurt us. Nevertheless, there is everything to play for in the second leg."
