Dortmund are unbeaten in the Bundesliga this season and hold a four-point lead at the top heading into the blockbuster clash at Signal Iduna Park.
Hoeness said Bayern would go into the encounter as outsiders after Dortmund's impressive start to the campaign.
"You can't go to Dortmund and say that you want to secure three points. Dortmund have had a very good season so far, no doubt about it," he said after Bayern's 2-0 win over AEK Athens in the Champions League on Wednesday.
"We do not go to Dortmund as favourites, but as underdogs – for the first time in a long time.
"We have to make sure we play a good game there and then we'll see what happens."
Robert Lewandowski's brace helped Bayern past AEK to slightly ease the pressure on under-fire coach Niko Kovac.
Hoeness called for patience with Bayern and criticised the media, particularly with the Bundesliga title race appearing set to be entertaining this campaign.
"Don't always be so negative. The season has just begun, we have a team in transition, a young coach who has to settle in here and you have to be patient," he said.
"Four weeks ago you all complained that the Bundesliga is getting boring again and now it is no longer boring but exciting and now that doesn't suit you.
"At some point you should agree on what you actually want. We're doing you a few favours right now."
Despite a slow start to the season under Kovac, Bayern sit just four points back of league leaders Dortmund ahead of Saturday's showdown and enter the match riding a bit of confidence.
"Firstly, the win is very good for our confidence," Kovac said after the win over AEK. "Secondly, it's important that we created lots of chances.
"I'm happy for Lewandowski because he's a very important player for us. He had four chances and scored two, which is a good ratio."