Gnabry has been out of form for the past few weeks and a short trip to Paris' Fashion show last week after their 1-1 draw with RB Leipzig did little to improve his status in the team.
Several pictures of him dressed in expensive fashion brands posted on social media infuriated club bosses.
Gnabry did earn a starting spot in Tuesday's 1-1 draw with Koln but he was taken off at halftime, with Nagelsmann saying he would instead start Kingsley Coman (26) on Saturday.
(Gnabry) had the chance to show a reaction against Koln," Nagelsmann told a news conference. "Against Koln he was not outstanding so it is clear that this (trip to Paris) is magnified by the media."
"We had a good chat and I explained him my view of things and I told him the substitution against Koln was not because of the Paris trip but performance-related," Nagelsmann said.
"We have a player, King (Coman), on the bench and he has done really well and he will start tomorrow."
Bayern, top of the table on 36 points, have yet to win a league game this year, while fellow Champions League club Eintracht's good form has carried them up to fourth place, five points off Bayern.
"The atmosphere is as it is at Bayern when you don't win," Nagelsmann said. "The lads trained well since the Cologne game. No one is terribly sad nor is there any euphoria."
"A flow is developed subconsciously. It is developed when you have it over 90 minutes and not consciously thinking about how you can start a game well."
"From the start you have to play the game as if there is only one situation which can be decisive. That's how you develop this flow."
"Just talking about the attitude and the right mentality does not create it. These past two matches we did not have the necessary attitude over 90 minutes," he said.
