Watzke said that Dortmund have shown on a number of occasions in recent seasons that they can beat Bayern, but would prefer to face Real Madrid or Barcelona.
"The past few years have shown that we have won the odd game against Bayern," UEFA.com quotes Watzke as saying. "Maybe Uli Hoeness shouldn't feel so comfortable.
"The allure of the international competition lies in playing teams from other countries and as a result, I would be keen to see two German-Spanish encounters rather than a game against Bayern.
"The other three clubs are world class. There is no difference who we face."
Dortmund reached the semi-finals after a dramatic finish on Tuesday night when they scored twice in injury time.