Coach Jupp Heynckes has repeatedly highlighted Bayern's low conversion rate despite having scored 25 goals in nine league games and having conceded just one in a near perfect start to the season.
On Tuesday it was a similar story with the Bavarians dominating for long spells, missing a penalty and several clear chances and failing to open up what would have been an impressive lead after only three games.
The Bundesliga leaders, who have lost only once in all competitions this season, have extra motivation to do well in the Champions League with the final to be held in Munich next year.
"It is a strange feeling. You walk off satisfied for having gotten a point and dissatisfied because you could have won," said striker Mario Gomez, who saw his penalty saved on 49 minutes.
Bayern defender Holger Badstuber's own goal, when he deflected in a Christian Maggio cross, was only the second goal they have conceded all season but Bayern should have added to Toni Kroos' second-minute opener.
Gomez, Kroos and Thomas Muller squandered a handful of chances as Bayern failed to apply the killer touch to their fast-paced approach play.
"We would have preferred to win and given our game in the second half it would have been deserved," Heynckes said.
"Up until Napoli's equalisers [in the 39th minute] we did not allow anything at the back. In the second half we again took control of the game and dominated."
Bayern top their Champions League group on seven points from three games, with Napoli on five and Manchester City, 2-1 winners against Villarreal, on four. The Spaniards are without a point.
"Now we have two home games against Napoli and Villarreal and if we win both of them we will advance," Gomez said.
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