Last season's treble winners travel to Signal Iduna Park on Saturday, with Jurgen Klopp's men having already beaten Bayern in July's DFL Super Cup.
Gundogan, who is currently sidelined with a back problem, claims that 4-2 victory, coupled with Dortmund's performance in their 2-1 UEFA Champions League final defeat to Bayern in May, shows they have the ability to hurt the European and German champions.
"They are the toughest side in Germany and possibly all Europe," he told Kicker.
"But we showed in the Champions League final and in the Super Cup at the end of July that we are probably the only team around right now who can cause Bayern problems.
After their clash with Bayern, Dortmund host Napoli in the Champions League, knowing defeat could knock them out of the competition.
"Both of these games (against Bayern and Napoli) are crucially important. It would be sensational for us if we could get six points out of them," Gundogan continued, adding his eagerness to return to first-team action.
"I'm very, very impatient. It hurts to have to watch for so long, but it's going to take a bit of time yet."
