Nagelsmann has led Leipzig to the top of the table after his first three matches in charge, with Werner on target five times already in the league.
The Germany striker has long been linked with a move to Bayern, but will this weekend face his mooted suitors, seemingly set for a decisive role in the biggest match of the season so far.
"Individual quality can always be crucial, so it could be key for us if we have a Timo Werner in top form," Nagelsmann told a news conference on Thursday.
"He was very good in training [on Wednesday] and he will be a very important factor. He is able to really hurt Bayern."
Asked about Leipzig's aims for the weekend, the coach added: "We can talk about [a draw] in retrospect. I would like to win and go into the game with that approach."
But Nagelsmann was keen to remind the media the outcome of this match will not necessarily be decisive in the title race.
"Good results against Bayern can take you a long way, but you have to keep performing every week," he said. "If we win against Bayern and then lose every other game, it counts for nothing."
Leipzig have some injury concerns - Dayot Upamecano is "93 per cent" fit, but Patrik Schick is "a bit battered", Kevin Kampl continues to deal with an ankle issue while Tyler Adams remains sidelined with a groin injury.
On the other side, Bayern coach Niko Kovac suggested Thomas Muller could be selected instead if Philippe Coutinho is not fully fit following a long journey from Brazil duty in Los Angeles.
Nagelsmann admitted he suspects his counterpart will go one way and is prepping for that, though he does not believe either player will drastically change how the Bundesliga champions will play.
"Of course, we are thinking about it, but it does not change the whole style of Bayern Munich," Nagelsmann said.
"We will not go into detail about whether Coutinho or Muller starts. They are different players, but there are also parallels. Both are hard to contain.
"I have in my head which player I think he plays. I'm preparing for something."