WATCH Bayern v Borussia Dortmund LIVE on beIN SPORTS this Sunday from 2.30am (AEST) | via Foxtel, Kayo, Fetch & CONNECT
Bayern trails Dortmund by just one point at the Bundesliga summit but may have to do without Goretzka for Sunday's (AEDT) crucial Klassiker after the midfielder suffered an apparent ankle injury.
The Germany international initially went down and required treatment in the 29th minute before failing to continue as Hansi Flick sent on Felix Nmecha three minutes later at RheinEnergieStadion.
That was in a double substitution, the second part of which was not enforced as Emre Can replaced Florian Wirtz with Germany trailing 2-0 after early goals from Yannick Carrasco and Romelu Lukaku in Cologne.
A potentially title-deciding meeting with Dortmund will also mark Thomas Tuchel's first game in charge of Bayern, who brought in the former Chelsea coach after dismissing Julian Nagelsmann last week.
The Bundesliga champion will hope Goretzka soon returns to fitness, with the two-legged Champions League quarter-final against Manchester City also on the horizon.