The Bavarians, who had won 10 of their 11 league games this season, paid the price for a string of big name absences and a desire by coach Jupp Heynckes to rotate ahead of next week's Champions League clash against Valencia.
Forward Mario Mandzukic confirmed his superb form with his ninth league goal in the third minute before it was Bayern's turn to be stunned, a minute after the restart with Markus Feulner's long-range effort.
"This is no disaster," Bayern coach Jupp Heynckes told reporters. "You just cannot win every game. We can live with this draw.
"We could have added another after the 1-0 but instead we conceded the equaliser at the worst possible psychological moment for us (right after the restart)."
Eager to grab their 11th win in 12 league games, Bayern got off to a flying start with Croat Mandzukic tapping in a Toni Kroos cutback in the third minute before hosts Nuremberg's unusual 4-1-4-1 formation had any time to flourish.
Bayern coach Heynckes had to leave injured Luiz Gustavo, Franck Ribery and Arjen Robben in Munich and opted not to include Mario Gomez, back after ankle surgery in August.
Their absences were bitterly felt as Bayern enjoyed the lion's share of possession in the first half but lacked the creativity to convert it into chances.
It was Nuremberg's turn to catch Bayern cold a minute after the break with Feulner's 25-metre drive beating goalkeeper Manuel Neuer.
Timo Gebhart was sent off 14 minutes from time with a second booking after elbowing Bastian Schweinsteiger, spoiling an otherwise successful day for Nuremberg, who move up to 14th on 12 points.