It was open first period from both sides, with Yannick Ferreira Carrasco and Douglas Costa going close before Lewandowski spectacularly opened the scoring in the 28th minute.
The second period had a slower pace to it, with decent opportunities for Arjen Robben and Thiago, but the points were already secured.
Pride was the only thing up for grabs at the Allianz Arena, with both Bayern and Atleti progressing into the last 16 in second and first place respectively. Despite there been nothing to play for, Diego Simeone's side had two great chances to take the lead.
Their first sniff at goal came in the 10th minute, it was a great passing display from the visitors, which ended in Antoine Griezmann putting Carrasco through on goal. He only had Manuel Neur to beat, but the German stopper did well to get down and block the effort.
Carrasco followed that up six minutes with another great chance, the ball was played in from the left and the Belgian did well to get on the end of it but once again it was straight at Neur.
It was then the turn of Carlo Ancelotti's side to have a chance on Jan Oblak's goal. Renato Sanches played a delightful ball into the path of Costa, who decided to shoot from a narrow angle. His shot was parried back into his path by Oblak, but his cross back into the mixer couldn't be met.
Scoring in style
Bayern had their tails up from that point, and it didn't take long for them to gain the advantage.
Lewandowski stood over the free-kick 20 yards from goal, and the Pole's technique was brilliant as he curled it into the top corner, giving Oblak no chance, and his first goal at the Allianz Arena since October.
Failing to get in gear
The second period didn't really get going in the early periods, with Robben pulling the strings after the restart. It was a quick counter-attacking move in the 55th minute which sas Robben through on goal. However the Dutchman checked back onto his left and the effort was deflected wide. Costa was on the end of the subsequent corner, but the volley was straight at Oblak.
The Dutchman was livid moments later, he managed to get to the by-line before the ball eventually came to Juan Bernat, but the effort was once again straight at Oblak. Replays showed that Stefan Savic had his arm across Robben, but it wasn't enough for Clement Turpin to point to the spot.
Seeing it out
It was clear that Ancelotti's side were looking to see out the rest of the contest, but had one final opportunity to finish off their Spanish counterparts.
It was yet another brilliant move from the German's, with the ball ending up at the feet of Costa. He did well to get the ball into the feet of Thiago, but he managed to scoop the effort over the crossbar from six yards out.