The visitors broke the deadlock after just 10 minutes as David Alaba's cross from the left flank found Lewandowski, who slid the ball into the bottom corner.
Benfica went clsoe to pulling themselves level in the 28th minute through Salvio, who forced Manuel Neuer into a fine save at his near post.
Bayern should have doubled their lead five minutes before the break when Franck Ribery played in Arjen Robben, who only had the goalkeeper to beat, but the Dutchman failed to convert.
The visitors didn't have wait that long for a second goal as Renato Sanches doubled the lead in the 55th minute with a good finish from close range against his former side.
Bayern thought they had a third goal in the 69th minute but Serge Gnabry's strike was ruled out for offside after some impressive build up play.
With the visitors comfortably leading, coach Niko Kovac introduced Leon Goretzka for James Rodriguez as they looked to shut up shop.
Robben could have bagged a third goal with the final kick of the game, but he drilled his effort straight at the goalkeeper as the encounter 2-0.