In a game that had very little chances in truth, the Old Lady were much the better team during the game and they got themselves in front when Vedad Ibisevic finally scored in the league to send the home crowd wild.
Just as it looked like the hosts were going to see the victory home, Lewandowski, on as a second half substitute, rescued Carlo Ancelotti's in the 6th minute of added on time to break the home sides hearts.
The result means for now that the Old Lady stay 6th place while Bayern stay top of the table before the rest of games this weekend finish tomorrow.
Both teams made a fast start to the game with the hosts taking an early lead as Ibisevic broke his goalscoring drought
Straight away from start of the game the tempo was fast as both sides looked to get off to a perfect start but both sides struggled to create anything of note early on.
Then all of a sudden, the hosts managed to get themselves in front. The goal though was one that the visitors weren't happy with. The reason for this was that the free kick that the goal came from shouldn't have been awarded.
From this free kick, Marvin Plattenhardt played a great ball into the box and Ibisevic got himself in front of his marker and put the ball into the back of the net to give the the hosts the crucial first goal.
Jarstein kept the visitors at bay with a number of crucial saves
The league leaders though started to take control of the game after going behind but only managed to have a couple of efforts on goal that Rune Jarstein kept out of the goal.
Firstly, from an Arjen Robben free-kick, Mats Hummels got a header on the ball towards goal but the keeper kept it out to the delight of the home fans.
Robben himself tested the keeper soon after with a good shot from the edge of the box but apart from that, it was a totally different Bayern performance from the one that dismantled Arsenal in midweek in the first half of the game but it was all to the credit of the hosts, who showed they were right up for the task.
The hosts continued on from were they left off in the first half by frustrating the visitors and they almost went two goals in front but Manuel Neuer denied Vladimír Darida from the edge of the box.
As the half went on the defending from the hosts got even stronger as Bayern just couldn't break through them and even when the hosts defence was beaten, Jarstein stood strong as he kept a very good free kick from David Alaba near the end of the game.
Lewandowski popped up with a goal in the 6th minute of injury to rescue a point for Bayern
Just as the home side thought that they had finally got over the line with a victory against Bayern, they were left stunned as the visitors got an equaliser in the six-minute off added on time.
The free kick was taken by Douglas Costa, who found Robben in space in the box but his goalbound shot was blocked, before Lewandowski, on as a second half substitution, stabbed the ball home on the rebound to earn the defending champions an unlikely point in a game that looked like a second defeat of the season for Ancelotti's side in the league.